A novel method of fuzzy fault tree analysis combined with VB program to identify and assess the risk of coal dust explosions.

PubMed

Wang, Hetang; Li, Jia; Wang, Deming; Huang, Zonghou

2017-01-01

Coal dust explosions (CDE) are one of the main threats to the occupational safety of coal miners. Aiming to identify and assess the risk of CDE, this paper proposes a novel method of fuzzy fault tree analysis combined with the Visual Basic (VB) program. In this methodology, various potential causes of the CDE are identified and a CDE fault tree is constructed. To overcome drawbacks from the lack of exact probability data for the basic events, fuzzy set theory is employed and the probability data of each basic event is treated as intuitionistic trapezoidal fuzzy numbers. In addition, a new approach for calculating the weighting of each expert is also introduced in this paper to reduce the error during the expert elicitation process. Specifically, an in-depth quantitative analysis of the fuzzy fault tree, such as the importance measure of the basic events and the cut sets, and the CDE occurrence probability is given to assess the explosion risk and acquire more details of the CDE. The VB program is applied to simplify the analysis process. A case study and analysis is provided to illustrate the effectiveness of this proposed method, and some suggestions are given to take preventive measures in advance and avoid CDE accidents.

Prospective identification of adolescent suicide ideation using classification tree analysis: Models for community-based screening.

PubMed

Hill, Ryan M; Oosterhoff, Benjamin; Kaplow, Julie B

2017-07-01

Although a large number of risk markers for suicide ideation have been identified, little guidance has been provided to prospectively identify adolescents at risk for suicide ideation within community settings. The current study addressed this gap in the literature by utilizing classification tree analysis (CTA) to provide a decision-making model for screening adolescents at risk for suicide ideation. Participants were N = 4,799 youth (Mage = 16.15 years, SD = 1.63) who completed both Waves 1 and 2 of the National Longitudinal Study of Adolescent to Adult Health. CTA was used to generate a series of decision rules for identifying adolescents at risk for reporting suicide ideation at Wave 2. Findings revealed 3 distinct solutions with varying sensitivity and specificity for identifying adolescents who reported suicide ideation. Sensitivity of the classification trees ranged from 44.6% to 77.6%. The tree with greatest specificity and lowest sensitivity was based on a history of suicide ideation. The tree with moderate sensitivity and high specificity was based on depressive symptoms, suicide attempts or suicide among family and friends, and social support. The most sensitive but least specific tree utilized these factors and gender, ethnicity, hours of sleep, school-related factors, and future orientation. These classification trees offer community organizations options for instituting large-scale screenings for suicide ideation risk depending on the available resources and modality of services to be provided. This study provides a theoretically and empirically driven model for prospectively identifying adolescents at risk for suicide ideation and has implications for preventive interventions among at-risk youth. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Spatial statistical analysis of tree deaths using airborne digital imagery

NASA Astrophysics Data System (ADS)

Chang, Ya-Mei; Baddeley, Adrian; Wallace, Jeremy; Canci, Michael

2013-04-01

High resolution digital airborne imagery offers unprecedented opportunities for observation and monitoring of vegetation, providing the potential to identify, locate and track individual vegetation objects over time. Analytical tools are required to quantify relevant information. In this paper, locations of trees over a large area of native woodland vegetation were identified using morphological image analysis techniques. Methods of spatial point process statistics were then applied to estimate the spatially-varying tree death risk, and to show that it is significantly non-uniform. [Tree deaths over the area were detected in our previous work (Wallace et al., 2008).] The study area is a major source of ground water for the city of Perth, and the work was motivated by the need to understand and quantify vegetation changes in the context of water extraction and drying climate. The influence of hydrological variables on tree death risk was investigated using spatial statistics (graphical exploratory methods, spatial point pattern modelling and diagnostics).

Terpenoid Variations within and among Half-Sibling Avocado Trees, Persea americana Mill. (Lauraceae)

PubMed Central

Niogret, Jerome; Epsky, Nancy D.; Schnell, Raymond J.; Boza, Edward J.; Kendra, Paul E.; Heath, Robert R.

2013-01-01

Chemical analyses were conducted to determine the qualitative and quantitative differences in monoterpenes and sesquiterpenes in plant material from avocado trees, Persea americana Mill. (Lauraceae). The initial study analyzed plant material sampled from the trunk to the leaves through different branch diameters to quantify proximo-distal spatial differences within a tree. All trees were seedlings initiated from a single maternal tree. Two-way analysis of variance was conducted on 34 chemicals that comprised at least 3% of the total chemical content of at least one tree and/or location within a tree. There were significant interactions between genotype and location sampled for most chemicals. Parentage analysis using microsatellite molecular markers (SSR's) determined that the four trees had three fathers and that they represented two full-siblings and two half-sibling trees. Descriptive discriminant analysis found that both genotype and location within a tree could be separated based on chemical content, and that the chemical content from full-siblings tended to be more similar than chemical content from half-siblings. To further explore the relationship between genetic background and chemical content, samples were analyzed from leaf material from 20 trees that included two sets of full-sibling seedling trees, the maternal tree and the surviving paternal tree. Descriptive discriminant analysis found good separation between the two full-sibling groups, and that the separation was associated with chemistry of the parental trees. Six groups of chemicals were identified that explained the variation among the trees. We discuss the results in relation to the discrimination process used by wood-boring insects for site-selection on host trees, for tree selection among potential host trees, and the potential use of terpenoid chemical content in chemotaxonomy of avocado trees. PMID:24039994

Terpenoid variations within and among half-sibling avocado trees, Persea americana Mill. (Lauraceae).

PubMed

Niogret, Jerome; Epsky, Nancy D; Schnell, Raymond J; Boza, Edward J; Kendra, Paul E; Heath, Robert R

2013-01-01

Chemical analyses were conducted to determine the qualitative and quantitative differences in monoterpenes and sesquiterpenes in plant material from avocado trees, Persea americana Mill. (Lauraceae). The initial study analyzed plant material sampled from the trunk to the leaves through different branch diameters to quantify proximo-distal spatial differences within a tree. All trees were seedlings initiated from a single maternal tree. Two-way analysis of variance was conducted on 34 chemicals that comprised at least 3% of the total chemical content of at least one tree and/or location within a tree. There were significant interactions between genotype and location sampled for most chemicals. Parentage analysis using microsatellite molecular markers (SSR's) determined that the four trees had three fathers and that they represented two full-siblings and two half-sibling trees. Descriptive discriminant analysis found that both genotype and location within a tree could be separated based on chemical content, and that the chemical content from full-siblings tended to be more similar than chemical content from half-siblings. To further explore the relationship between genetic background and chemical content, samples were analyzed from leaf material from 20 trees that included two sets of full-sibling seedling trees, the maternal tree and the surviving paternal tree. Descriptive discriminant analysis found good separation between the two full-sibling groups, and that the separation was associated with chemistry of the parental trees. Six groups of chemicals were identified that explained the variation among the trees. We discuss the results in relation to the discrimination process used by wood-boring insects for site-selection on host trees, for tree selection among potential host trees, and the potential use of terpenoid chemical content in chemotaxonomy of avocado trees.

Enrolment Management in Graduate Business Programs: Predicting Student Retention

ERIC Educational Resources Information Center

Eshghi, Abdoloreza; Haughton, Dominique; Li, Mingfei; Senne, Linda; Skaletsky, Maria; Woolford, Sam

2011-01-01

The increasing competition for graduate students among business schools has resulted in a greater emphasis on graduate business student retention. In an effort to address this issue, the current article uses survival analysis, decision trees and TreeNet® to identify factors that can be used to identify students who are at risk of dropping out of a…

What Satisfies Students?: Mining Student-Opinion Data with Regression and Decision Tree Analysis

ERIC Educational Resources Information Center

Thomas, Emily H.; Galambos, Nora

2004-01-01

To investigate how students' characteristics and experiences affect satisfaction, this study uses regression and decision tree analysis with the CHAID algorithm to analyze student-opinion data. A data mining approach identifies the specific aspects of students' university experience that most influence three measures of general satisfaction. The…

Evidence of solar activity and El Niño signals in tree rings of Araucaria araucana and A. angustifolia in South America

NASA Astrophysics Data System (ADS)

Perone, A.; Lombardi, F.; Marchetti, M.; Tognetti, R.; Lasserre, B.

2016-10-01

Tree rings reveal climatic variations through years, but also the effect of solar activity in influencing the climate on a large scale. In order to investigate the role of solar cycles on climatic variability and to analyse their influences on tree growth, we focused on tree-ring chronologies of Araucaria angustifolia and Araucaria araucana in four study areas: Irati and Curitiba in Brazil, Caviahue in Chile, and Tolhuaca in Argentina. We obtained an average tree-ring chronology of 218, 117, 439, and 849 years for these areas, respectively. Particularly, the older chronologies also included the period of the Maunder and Dalton minima. To identify periodicities and trends observable in tree growth, the time series were analysed using spectral, wavelet and cross-wavelet techniques. Analysis based on the Multitaper method of annual growth rates identified 2 cycles with periodicities of 11 (Schwebe cycle) and 5.5 years (second harmonic of Schwebe cycle). In the Chilean and Argentinian sites, significant agreement between the time series of tree rings and the 11-year solar cycle was found during the periods of maximum solar activity. Results also showed oscillation with periods of 2-7 years, probably induced by local environmental variations, and possibly also related to the El-Niño events. Moreover, the Morlet complex wavelet analysis was applied to study the most relevant variability factors affecting tree-ring time series. Finally, we applied the cross-wavelet spectral analysis to evaluate the time lags between tree-ring and sunspot-number time series, as well as for the interaction between tree rings, the Southern Oscillation Index (SOI) and temperature and precipitation. Trees sampled in Chile and Argentina showed more evident responses of fluctuations in tree-ring time series to the variations of short and long periodicities in comparison with the Brazilian ones. These results provided new evidence on the solar activity-climate pattern-tree ring connections over centuries.

A retrospective analysis to identify the factors affecting infection in patients undergoing chemotherapy.

PubMed

Park, Ji Hyun; Kim, Hyeon-Young; Lee, Hanna; Yun, Eun Kyoung

2015-12-01

This study compares the performance of the logistic regression and decision tree analysis methods for assessing the risk factors for infection in cancer patients undergoing chemotherapy. The subjects were 732 cancer patients who were receiving chemotherapy at K university hospital in Seoul, Korea. The data were collected between March 2011 and February 2013 and were processed for descriptive analysis, logistic regression and decision tree analysis using the IBM SPSS Statistics 19 and Modeler 15.1 programs. The most common risk factors for infection in cancer patients receiving chemotherapy were identified as alkylating agents, vinca alkaloid and underlying diabetes mellitus. The logistic regression explained 66.7% of the variation in the data in terms of sensitivity and 88.9% in terms of specificity. The decision tree analysis accounted for 55.0% of the variation in the data in terms of sensitivity and 89.0% in terms of specificity. As for the overall classification accuracy, the logistic regression explained 88.0% and the decision tree analysis explained 87.2%. The logistic regression analysis showed a higher degree of sensitivity and classification accuracy. Therefore, logistic regression analysis is concluded to be the more effective and useful method for establishing an infection prediction model for patients undergoing chemotherapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

NASA Astrophysics Data System (ADS)

Gao, Zhiyun; Grout, Randall W.; Hoffman, Eric A.; Saha, Punam K.

2012-02-01

Diseases like pulmonary embolism and pulmonary hypertension are associated with vascular dystrophy. Identifying such pulmonary artery/vein (A/V) tree dystrophy in terms of quantitative measures via CT imaging significantly facilitates early detection of disease or a treatment monitoring process. A tree structure, consisting of nodes and connected arcs, linked to the volumetric representation allows multi-level geometric and volumetric analysis of A/V trees. Here, a new theory and method is presented to generate multi-level A/V tree representation of volumetric data and to compute quantitative measures of A/V tree geometry and topology at various tree hierarchies. The new method is primarily designed on arc skeleton computation followed by a tree construction based topologic and geometric analysis of the skeleton. The method starts with a volumetric A/V representation as input and generates its topologic and multi-level volumetric tree representations long with different multi-level morphometric measures. A new recursive merging and pruning algorithms are introduced to detect bad junctions and noisy branches often associated with digital geometric and topologic analysis. Also, a new notion of shortest axial path is introduced to improve the skeletal arc joining two junctions. The accuracy of the multi-level tree analysis algorithm has been evaluated using computer generated phantoms and pulmonary CT images of a pig vessel cast phantom while the reproducibility of method is evaluated using multi-user A/V separation of in vivo contrast-enhanced CT images of a pig lung at different respiratory volumes.

Characterizing individual particles on tree leaves using computer automated scanning electron microscopy

Treesearch

D. L. Johnson; D. J. Nowak; V. A. Jouraeva

1999-01-01

Leaves from twenty-three deciduous tree species and five conifer species were collected within a limited geographic range (1 km radius) and evaluated for possible application of scanning electron microscopy and X-ray microanalysis techniques of individual particle analysis (IPA). The goal was to identify tree species with leaves suitable for the automated...

Prioritizing preferable locations for increasing urban tree canopy in New York City

Treesearch

Dexter Locke; J. Morgan Grove; Jacqueline W.T. Lu; Austin Troy; Jarlath P.M. O' Neil-Dunne; Brian Beck

2010-01-01

This paper presents a set of Geographic Information System (GIS) methods for identifying and prioritizing tree planting sites in urban environments. It uses an analytical approach created by a University of Vermont service-learning class called "GIS Analysis of New York City's Ecology" that was designed to provide research support to the MillionTreesNYC...

Identifying influential factors of business process performance using dependency analysis

NASA Astrophysics Data System (ADS)

Wetzstein, Branimir; Leitner, Philipp; Rosenberg, Florian; Dustdar, Schahram; Leymann, Frank

2011-02-01

We present a comprehensive framework for identifying influential factors of business process performance. In particular, our approach combines monitoring of process events and Quality of Service (QoS) measurements with dependency analysis to effectively identify influential factors. The framework uses data mining techniques to construct tree structures to represent dependencies of a key performance indicator (KPI) on process and QoS metrics. These dependency trees allow business analysts to determine how process KPIs depend on lower-level process metrics and QoS characteristics of the IT infrastructure. The structure of the dependencies enables a drill-down analysis of single factors of influence to gain a deeper knowledge why certain KPI targets are not met.

Chi-squared Automatic Interaction Detection Decision Tree Analysis of Risk Factors for Infant Anemia in Beijing, China

PubMed Central

Ye, Fang; Chen, Zhi-Hua; Chen, Jie; Liu, Fang; Zhang, Yong; Fan, Qin-Ying; Wang, Lin

2016-01-01

Background: In the past decades, studies on infant anemia have mainly focused on rural areas of China. With the increasing heterogeneity of population in recent years, available information on infant anemia is inconclusive in large cities of China, especially with comparison between native residents and floating population. This population-based cross-sectional study was implemented to determine the anemic status of infants as well as the risk factors in a representative downtown area of Beijing. Methods: As useful methods to build a predictive model, Chi-squared automatic interaction detection (CHAID) decision tree analysis and logistic regression analysis were introduced to explore risk factors of infant anemia. A total of 1091 infants aged 6–12 months together with their parents/caregivers living at Heping Avenue Subdistrict of Beijing were surveyed from January 1, 2013 to December 31, 2014. Results: The prevalence of anemia was 12.60% with a range of 3.47%–40.00% in different subgroup characteristics. The CHAID decision tree model has demonstrated multilevel interaction among risk factors through stepwise pathways to detect anemia. Besides the three predictors identified by logistic regression model including maternal anemia during pregnancy, exclusive breastfeeding in the first 6 months, and floating population, CHAID decision tree analysis also identified the fourth risk factor, the maternal educational level, with higher overall classification accuracy and larger area below the receiver operating characteristic curve. Conclusions: The infant anemic status in metropolis is complex and should be carefully considered by the basic health care practitioners. CHAID decision tree analysis has demonstrated a better performance in hierarchical analysis of population with great heterogeneity. Risk factors identified by this study might be meaningful in the early detection and prompt treatment of infant anemia in large cities. PMID:27174328

Chi-squared Automatic Interaction Detection Decision Tree Analysis of Risk Factors for Infant Anemia in Beijing, China.

PubMed

Ye, Fang; Chen, Zhi-Hua; Chen, Jie; Liu, Fang; Zhang, Yong; Fan, Qin-Ying; Wang, Lin

2016-05-20

In the past decades, studies on infant anemia have mainly focused on rural areas of China. With the increasing heterogeneity of population in recent years, available information on infant anemia is inconclusive in large cities of China, especially with comparison between native residents and floating population. This population-based cross-sectional study was implemented to determine the anemic status of infants as well as the risk factors in a representative downtown area of Beijing. As useful methods to build a predictive model, Chi-squared automatic interaction detection (CHAID) decision tree analysis and logistic regression analysis were introduced to explore risk factors of infant anemia. A total of 1091 infants aged 6-12 months together with their parents/caregivers living at Heping Avenue Subdistrict of Beijing were surveyed from January 1, 2013 to December 31, 2014. The prevalence of anemia was 12.60% with a range of 3.47%-40.00% in different subgroup characteristics. The CHAID decision tree model has demonstrated multilevel interaction among risk factors through stepwise pathways to detect anemia. Besides the three predictors identified by logistic regression model including maternal anemia during pregnancy, exclusive breastfeeding in the first 6 months, and floating population, CHAID decision tree analysis also identified the fourth risk factor, the maternal educational level, with higher overall classification accuracy and larger area below the receiver operating characteristic curve. The infant anemic status in metropolis is complex and should be carefully considered by the basic health care practitioners. CHAID decision tree analysis has demonstrated a better performance in hierarchical analysis of population with great heterogeneity. Risk factors identified by this study might be meaningful in the early detection and prompt treatment of infant anemia in large cities.

A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis.

PubMed

Seidel, Dominik

2018-01-01

The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic approach is presented that enables to calculate the box dimension as a measure of structural complexity of individual trees using fractal analysis. It was found that the box dimension of trees was significantly different among the tested species, among trees belonging to the same species but exposed to different growing conditions (at gap vs. forest interior) or to different kinds of competition (intraspecific vs. interspecific). Furthermore, it was shown that the box dimension is positively related to the trees' growth rate. The box dimension was identified as an easy to calculate measure that integrates the effect of several external drivers of tree structure, such as competition strength and type, while simultaneously providing information on structure-related properties, like tree growth.

An improved classification tree analysis of high cost modules based upon an axiomatic definition of complexity

NASA Technical Reports Server (NTRS)

Tian, Jianhui; Porter, Adam; Zelkowitz, Marvin V.

1992-01-01

Identification of high cost modules has been viewed as one mechanism to improve overall system reliability, since such modules tend to produce more than their share of problems. A decision tree model was used to identify such modules. In this current paper, a previously developed axiomatic model of program complexity is merged with the previously developed decision tree process for an improvement in the ability to identify such modules. This improvement was tested using data from the NASA Software Engineering Laboratory.

Extensive characterization of Tupaia belangeri neuropeptidome using an integrated mass spectrometric approach.

PubMed

Petruzziello, Filomena; Fouillen, Laetitia; Wadensten, Henrik; Kretz, Robert; Andren, Per E; Rainer, Gregor; Zhang, Xiaozhe

2012-02-03

Neuropeptidomics is used to characterize endogenous peptides in the brain of tree shrews (Tupaia belangeri). Tree shrews are small animals similar to rodents in size but close relatives of primates, and are excellent models for brain research. Currently, tree shrews have no complete proteome information available on which direct database search can be allowed for neuropeptide identification. To increase the capability in the identification of neuropeptides in tree shrews, we developed an integrated mass spectrometry (MS)-based approach that combines methods including data-dependent, directed, and targeted liquid chromatography (LC)-Fourier transform (FT)-tandem MS (MS/MS) analysis, database construction, de novo sequencing, precursor protein search, and homology analysis. Using this integrated approach, we identified 107 endogenous peptides that have sequences identical or similar to those from other mammalian species. High accuracy MS and tandem MS information, with BLAST analysis and chromatographic characteristics were used to confirm the sequences of all the identified peptides. Interestingly, further sequence homology analysis demonstrated that tree shrew peptides have a significantly higher degree of homology to equivalent sequences in humans than those in mice or rats, consistent with the close phylogenetic relationship between tree shrews and primates. Our results provide the first extensive characterization of the peptidome in tree shrews, which now permits characterization of their function in nervous and endocrine system. As the approach developed fully used the conservative properties of neuropeptides in evolution and the advantage of high accuracy MS, it can be portable for identification of neuropeptides in other species for which the fully sequenced genomes or proteomes are not available.

Differential expression proteins associated with bud dormancy release during chilling treatment of tree peony (Paeonia suffruticosa).

PubMed

Zhang, Y X; Yu, D; Tian, X L; Liu, C Y; Gai, S P; Zheng, G S

2015-01-01

Endo-dormant flower buds of tree peony must have sufficient chilling duration to reinitiate growth, which is a major obstacle to the forcing culture of tree peony in winter. We used a combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionisation time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) to identify the differentially expressed proteins of tree peony after three different chilling treatments: endo-dormancy, endo-dormancy release and eco-dormancy stages. More than 200 highly reproducible protein spots were detected, and 31 differentially expressed spots (P < 0.05) were selected for further analysis. Finally, 20 protein spots were confidently identified from databases, which were annotated and classified into seven functional categories: response to abiotic or biotic stimulus (four), metabolic processes (four), other binding (three), transcription or transcription regulation (two), biological processes (one), cell biogenesis (one) and unclassified (five). The results of qPCR of five genes were mainly consistent with that of the protein accumulation analysis as determined by 2-DE. This indicated that most of these genes were mainly regulated at transcriptional level. The activity of nitrate reductase and pyruvate dehydrogenase E1 was consistent with the 2-DE results. The proteomic profiles indicated activation of citrate cycle, amino acid metabolism, lipid metabolism, energy production, calcium signalling and cell growth processes by chilling fulfilment to facilitate dormancy release in tree peony. Analysis of functions of identified proteins will increase our knowledge of endo-dormancy release in tree peony. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

What Satisfies Students? Mining Student-Opinion Data with Regression and Decision-Tree Analysis. AIR 2002 Forum Paper.

ERIC Educational Resources Information Center

Thomas, Emily H.; Galambos, Nora

To investigate how students' characteristics and experiences affect satisfaction, this study used regression and decision-tree analysis with the CHAID algorithm to analyze student opinion data from a sample of 1,783 college students. A data-mining approach identifies the specific aspects of students' university experience that most influence three…

Long-term sustainability in Davis Late Successional Reserve

Treesearch

Jim Stone; Joan Kittrell

2004-01-01

A pilot watershed analysis along with the Davis Late Successional Reserve analysis in the range of the northern spotted owl identified potential loss of suitable habitat, reduction in the numbers of large trees, and lack of replacements for large trees. A variety of silvicultural thinning techniques has been used to address these important issues and to move toward a...

Fire safety in transit systems fault tree analysis

DOT National Transportation Integrated Search

1981-09-01

Fire safety countermeasures applicable to transit vehicles are identified and evaluated. This document contains fault trees which illustrate the sequences of events which may lead to a transit-fire related casualty. A description of the basis for the...

An evaluation of the STEMS tree growth projection system.

Treesearch

Margaret R. Holdaway; Gary J. Brand

1983-01-01

STEMS (Stand and Tree Evaluation and Modeling System) is a tree growth projection system. This paper (1) compares the performance of the current version of STEMS developed for the Lake States with that of the original model and (2) reports the results of an analysis of the current model over a wide range of conditions and identifies its main strengths and weaknesses...

Decision tree analysis to stratify risk of de novo non-melanoma skin cancer following liver transplantation.

PubMed

Tanaka, Tomohiro; Voigt, Michael D

2018-03-01

Non-melanoma skin cancer (NMSC) is the most common de novo malignancy in liver transplant (LT) recipients; it behaves more aggressively and it increases mortality. We used decision tree analysis to develop a tool to stratify and quantify risk of NMSC in LT recipients. We performed Cox regression analysis to identify which predictive variables to enter into the decision tree analysis. Data were from the Organ Procurement Transplant Network (OPTN) STAR files of September 2016 (n = 102984). NMSC developed in 4556 of the 105984 recipients, a mean of 5.6 years after transplant. The 5/10/20-year rates of NMSC were 2.9/6.3/13.5%, respectively. Cox regression identified male gender, Caucasian race, age, body mass index (BMI) at LT, and sirolimus use as key predictive or protective factors for NMSC. These factors were entered into a decision tree analysis. The final tree stratified non-Caucasians as low risk (0.8%), and Caucasian males > 47 years, BMI < 40 who did not receive sirolimus, as high risk (7.3% cumulative incidence of NMSC). The predictions in the derivation set were almost identical to those in the validation set (r 2  = 0.971, p < 0.0001). Cumulative incidence of NMSC in low, moderate and high risk groups at 5/10/20 year was 0.5/1.2/3.3, 2.1/4.8/11.7 and 5.6/11.6/23.1% (p < 0.0001). The decision tree model accurately stratifies the risk of developing NMSC in the long-term after LT.

Decision-Tree Analysis for Predicting First-Time Pass/Fail Rates for the NCLEX-RN® in Associate Degree Nursing Students.

PubMed

Chen, Hsiu-Chin; Bennett, Sean

2016-08-01

Little evidence shows the use of decision-tree algorithms in identifying predictors and analyzing their associations with pass rates for the NCLEX-RN(®) in associate degree nursing students. This longitudinal and retrospective cohort study investigated whether a decision-tree algorithm could be used to develop an accurate prediction model for the students' passing or failing the NCLEX-RN. This study used archived data from 453 associate degree nursing students in a selected program. The chi-squared automatic interaction detection analysis of the decision trees module was used to examine the effect of the collected predictors on passing/failing the NCLEX-RN. The actual percentage scores of Assessment Technologies Institute®'s RN Comprehensive Predictor(®) accurately identified students at risk of failing. The classification model correctly classified 92.7% of the students for passing. This study applied the decision-tree model to analyze a sequence database for developing a prediction model for early remediation in preparation for the NCLEXRN. [J Nurs Educ. 2016;55(8):454-457.]. Copyright 2016, SLACK Incorporated.

The process and utility of classification and regression tree methodology in nursing research

PubMed Central

Kuhn, Lisa; Page, Karen; Ward, John; Worrall-Carter, Linda

2014-01-01

Aim This paper presents a discussion of classification and regression tree analysis and its utility in nursing research. Background Classification and regression tree analysis is an exploratory research method used to illustrate associations between variables not suited to traditional regression analysis. Complex interactions are demonstrated between covariates and variables of interest in inverted tree diagrams. Design Discussion paper. Data sources English language literature was sourced from eBooks, Medline Complete and CINAHL Plus databases, Google and Google Scholar, hard copy research texts and retrieved reference lists for terms including classification and regression tree* and derivatives and recursive partitioning from 1984–2013. Discussion Classification and regression tree analysis is an important method used to identify previously unknown patterns amongst data. Whilst there are several reasons to embrace this method as a means of exploratory quantitative research, issues regarding quality of data as well as the usefulness and validity of the findings should be considered. Implications for Nursing Research Classification and regression tree analysis is a valuable tool to guide nurses to reduce gaps in the application of evidence to practice. With the ever-expanding availability of data, it is important that nurses understand the utility and limitations of the research method. Conclusion Classification and regression tree analysis is an easily interpreted method for modelling interactions between health-related variables that would otherwise remain obscured. Knowledge is presented graphically, providing insightful understanding of complex and hierarchical relationships in an accessible and useful way to nursing and other health professions. PMID:24237048

The process and utility of classification and regression tree methodology in nursing research.

PubMed

Kuhn, Lisa; Page, Karen; Ward, John; Worrall-Carter, Linda

2014-06-01

This paper presents a discussion of classification and regression tree analysis and its utility in nursing research. Classification and regression tree analysis is an exploratory research method used to illustrate associations between variables not suited to traditional regression analysis. Complex interactions are demonstrated between covariates and variables of interest in inverted tree diagrams. Discussion paper. English language literature was sourced from eBooks, Medline Complete and CINAHL Plus databases, Google and Google Scholar, hard copy research texts and retrieved reference lists for terms including classification and regression tree* and derivatives and recursive partitioning from 1984-2013. Classification and regression tree analysis is an important method used to identify previously unknown patterns amongst data. Whilst there are several reasons to embrace this method as a means of exploratory quantitative research, issues regarding quality of data as well as the usefulness and validity of the findings should be considered. Classification and regression tree analysis is a valuable tool to guide nurses to reduce gaps in the application of evidence to practice. With the ever-expanding availability of data, it is important that nurses understand the utility and limitations of the research method. Classification and regression tree analysis is an easily interpreted method for modelling interactions between health-related variables that would otherwise remain obscured. Knowledge is presented graphically, providing insightful understanding of complex and hierarchical relationships in an accessible and useful way to nursing and other health professions. © 2013 The Authors. Journal of Advanced Nursing Published by John Wiley & Sons Ltd.

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

PubMed Central

2013-01-01

Background Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by one of the Neonectria species of fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees. Results Proteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified. Conclusions Further study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services. PMID:23317283

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

PubMed

Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

2015-12-01

In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

A novel approach to internal crown characterization for coniferous tree species classification

NASA Astrophysics Data System (ADS)

Harikumar, A.; Bovolo, F.; Bruzzone, L.

2016-10-01

The knowledge about individual trees in forest is highly beneficial in forest management. High density small foot- print multi-return airborne Light Detection and Ranging (LiDAR) data can provide a very accurate information about the structural properties of individual trees in forests. Every tree species has a unique set of crown structural characteristics that can be used for tree species classification. In this paper, we use both the internal and external crown structural information of a conifer tree crown, derived from a high density small foot-print multi-return LiDAR data acquisition for species classification. Considering the fact that branches are the major building blocks of a conifer tree crown, we obtain the internal crown structural information using a branch level analysis. The structure of each conifer branch is represented using clusters in the LiDAR point cloud. We propose the joint use of the k-means clustering and geometric shape fitting, on the LiDAR data projected onto a novel 3-dimensional space, to identify branch clusters. After mapping the identified clusters back to the original space, six internal geometric features are estimated using a branch-level analysis. The external crown characteristics are modeled by using six least correlated features based on cone fitting and convex hull. Species classification is performed using a sparse Support Vector Machines (sparse SVM) classifier.

Biochemical analysis of 'kerosene tree' Hymenaea courbaril L. under heat stress.

PubMed

Gupta, Dinesh; Eldakak, Moustafa; Rohila, Jai S; Basu, Chhandak

2014-01-01

Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, β ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants.

Observation of eight ancient olive trees (Olea europaea L.) growing in the Garden of Gethsemane.

PubMed

Petruccelli, Raffaella; Giordano, Cristiana; Salvatici, Maria Cristina; Capozzoli, Laura; Ciaccheri, Leonardo; Pazzini, Massimo; Lain, Orietta; Testolin, Raffaele; Cimato, Antonio

2014-05-01

For thousands of years, olive trees (Olea europaea L.) have been a significant presence and a symbol in the Garden of Gethsemane, a place located at the foot of the Mount of Olives, Jerusalem, remembered for the agony of Jesus Christ before his arrest. This investigation comprises the first morphological and genetic characterization of eight olive trees in the Garden of Gethsemane. Pomological traits, morphometric, and ultrastructural observations as well as SSR (Simple Sequence Repeat) analysis were performed to identify the olive trees. Statistical analyses were conducted to evaluate their morphological variability. The study revealed a low morphological variability and minimal dissimilarity among the olive trees. According to molecular analysis, these trees showed the same allelic profile at all microsatellite loci analyzed. Combining the results of the different analyses carried out in the frame of the present work, we could conclude that the eight olive trees of the Gethsemane Garden have been propagated from a single genotype. Copyright © 2014. Published by Elsevier SAS.

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

PubMed Central

2014-01-01

Background As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Results Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each “strategy” for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. Conclusions When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates. PMID:24678701

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines.

PubMed

DeGiorgio, Michael; Syring, John; Eckert, Andrew J; Liston, Aaron; Cronn, Richard; Neale, David B; Rosenberg, Noah A

2014-03-29

As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many methods for performing this inference has remained largely unexplored. Some methods have been proven to be consistent given certain evolutionary models, whereas others rely on criteria that, although appropriate for many parameter values, have peculiar zones of the parameter space in which they fail to converge on the correct estimate as data sets increase in size. Here, using North American pines, we empirically evaluate the behavior of 24 strategies for species tree inference using three alternative outgroups (72 strategies total). The data consist of 120 individuals sampled in eight ingroup species from subsection Strobus and three outgroup species from subsection Gerardianae, spanning ∼47 kilobases of sequence at 121 loci. Each "strategy" for inferring species trees consists of three features: a species tree construction method, a gene tree inference method, and a choice of outgroup. We use multivariate analysis techniques such as principal components analysis and hierarchical clustering to identify tree characteristics that are robustly observed across strategies, as well as to identify groups of strategies that produce trees with similar features. We find that strategies that construct species trees using only topological information cluster together and that strategies that use additional non-topological information (e.g., branch lengths) also cluster together. Strategies that utilize more than one individual within a species to infer gene trees tend to produce estimates of species trees that contain clades present in trees estimated by other strategies. Strategies that use the minimize-deep-coalescences criterion to construct species trees tend to produce species tree estimates that contain clades that are not present in trees estimated by the Concatenation, RTC, SMRT, STAR, and STEAC methods, and that in general are more balanced than those inferred by these other strategies. When constructing a species tree from a multilocus set of sequences, our observations provide a basis for interpreting differences in species tree estimates obtained via different approaches that have a two-stage structure in common, one step for gene tree estimation and a second step for species tree estimation. The methods explored here employ a number of distinct features of the data, and our analysis suggests that recovery of the same results from multiple methods that tend to differ in their patterns of inference can be a valuable tool for obtaining reliable estimates.

Identification of Powdery Mildew Responsive Genes in Hevea brasiliensis through mRNA Differential Display

PubMed Central

Li, Xiang; Bi, Zhenghong; Di, Rong; Liang, Peng; He, Qiguang; Liu, Wenbo; Miao, Weiguo; Zheng, Fucong

2016-01-01

Powdery mildew is an important disease of rubber trees caused by Oidium heveae B. A. Steinmann. As far as we know, none of the resistance genes related to powdery mildew have been isolated from the rubber tree. There is little information available at the molecular level regarding how a rubber tree develops defense mechanisms against this pathogen. We have studied rubber tree mRNA transcripts from the resistant RRIC52 cultivar by differential display analysis. Leaves inoculated with the spores of O. heveae were collected from 0 to 120 hpi in order to identify pathogen-regulated genes at different infection stages. We identified 78 rubber tree genes that were differentially expressed during the plant–pathogen interaction. BLAST analysis for these 78 ESTs classified them into seven functional groups: cell wall and membrane pathways, transcription factor and regulatory proteins, transporters, signal transduction, phytoalexin biosynthesis, other metabolism functions, and unknown functions. The gene expression for eight of these genes was validated by qRT-PCR in both RRIC52 and the partially susceptible Reyan 7-33-97 cultivars, revealing the similar or differential changes of gene expressions between these two cultivars. This study has improved our overall understanding of the molecular mechanisms of rubber tree resistance to powdery mildew. PMID:26840302

Spectral analysis of white ash response to emerald ash borer infestations

NASA Astrophysics Data System (ADS)

Calandra, Laura

The emerald ash borer (EAB) (Agrilus planipennis Fairmaire) is an invasive insect that has killed over 50 million ash trees in the US. The goal of this research was to establish a method to identify ash trees infested with EAB using remote sensing techniques at the leaf-level and tree crown level. First, a field-based study at the leaf-level used the range of spectral bands from the WorldView-2 sensor to determine if there was a significant difference between EAB-infested white ash (Fraxinus americana) and healthy leaves. Binary logistic regression models were developed using individual and combinations of wavelengths; the most successful model included 545 and 950 nm bands. The second half of this research employed imagery to identify healthy and EAB-infested trees, comparing pixel- and object-based methods by applying an unsupervised classification approach and a tree crown delineation algorithm, respectively. The pixel-based models attained the highest overall accuracies.

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

PubMed

duVerle, David A; Yotsukura, Sohiya; Nomura, Seitaro; Aburatani, Hiroyuki; Tsuda, Koji

2016-09-13

Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/ .

Survey of critical failure events in on-chip interconnect by fault tree analysis

NASA Astrophysics Data System (ADS)

Yokogawa, Shinji; Kunii, Kyousuke

2018-07-01

In this paper, a framework based on reliability physics is proposed for adopting fault tree analysis (FTA) to the on-chip interconnect system of a semiconductor. By integrating expert knowledge and experience regarding the possibilities of failure on basic events, critical issues of on-chip interconnect reliability will be evaluated by FTA. In particular, FTA is used to identify the minimal cut sets with high risk priority. Critical events affecting the on-chip interconnect reliability are identified and discussed from the viewpoint of long-term reliability assessment. The moisture impact is evaluated as an external event.

Enumerating all maximal frequent subtrees in collections of phylogenetic trees

PubMed Central

2014-01-01

Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474

Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

PubMed

Deepak, Akshay; Fernández-Baca, David

2014-01-01

A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.

[Mahalanobis distance based hyperspectral characteristic discrimination of leaves of different desert tree species].

PubMed

Lin, Hai-jun; Zhang, Hui-fang; Gao, Ya-qi; Li, Xia; Yang, Fan; Zhou, Yan-fei

2014-12-01

The hyperspectral reflectance of Populus euphratica, Tamarix hispida, Haloxylon ammodendron and Calligonum mongolicum in the lower reaches of Tarim River and Turpan Desert Botanical Garden was measured by using the HR-768 field-portable spectroradiometer. The method of continuum removal, first derivative reflectance and second derivative reflectance were used to deal with the original spectral data of four tree species. The method of Mahalanobis Distance was used to select the bands with significant differences in the original spectral data and transform spectral data to identify the different tree species. The progressive discrimination analyses were used to test the selective bands used to identify different tree species. The results showed that The Mahalanobis Distance method was an effective method in feature band extraction. The bands for identifying different tree species were most near-infrared bands. The recognition accuracy of four methods was 85%, 93.8%, 92.4% and 95.5% respectively. Spectrum transform could improve the recognition accuracy. The recognition accuracy of different research objects and different spectrum transform methods were different. The research provided evidence for desert tree species classification, monitoring biodiversity and the analysis of area in desert by using large scale remote sensing method.

A systematic risk management approach employed on the CloudSat project

NASA Technical Reports Server (NTRS)

Basilio, R. R.; Plourde, K. S.; Lam, T.

2000-01-01

The CloudSat Project has developed a simplified approach for fault tree analysis and probabilistic risk assessment. A system-level fault tree has been constructed to identify credible fault scenarios and failure modes leading up to a potential failure to meet the nominal mission success criteria.

Fuzzy fault tree assessment based on improved AHP for fire and explosion accidents for steel oil storage tanks.

PubMed

Shi, Lei; Shuai, Jian; Xu, Kui

2014-08-15

Fire and explosion accidents of steel oil storage tanks (FEASOST) occur occasionally during the petroleum and chemical industry production and storage processes and often have devastating impact on lives, the environment and property. To contribute towards the development of a quantitative approach for assessing the occurrence probability of FEASOST, a fault tree of FEASOST is constructed that identifies various potential causes. Traditional fault tree analysis (FTA) can achieve quantitative evaluation if the failure data of all of the basic events (BEs) are available, which is almost impossible due to the lack of detailed data, as well as other uncertainties. This paper makes an attempt to perform FTA of FEASOST by a hybrid application between an expert elicitation based improved analysis hierarchy process (AHP) and fuzzy set theory, and the occurrence possibility of FEASOST is estimated for an oil depot in China. A comparison between statistical data and calculated data using fuzzy fault tree analysis (FFTA) based on traditional and improved AHP is also made. Sensitivity and importance analysis has been performed to identify the most crucial BEs leading to FEASOST that will provide insights into how managers should focus effective mitigation. Copyright © 2014 Elsevier B.V. All rights reserved.

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

PubMed Central

Aberer, Andre J.; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

Abstract The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees. PMID:22962004

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice.

PubMed

Aberer, Andre J; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

PubMed Central

Minh, Bui Quang; von Haeseler, Arndt

2015-01-01

Abstract In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original “full” terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference. PMID:26448206

Planning effectiveness may grow on fault trees.

PubMed

Chow, C W; Haddad, K; Mannino, B

1991-10-01

The first step of a strategic planning process--identifying and analyzing threats and opportunities--requires subjective judgments. By using an analytical tool known as a fault tree, healthcare administrators can reduce the unreliability of subjective decision making by creating a logical structure for problem solving and decision making. A case study of 11 healthcare administrators showed that an analysis technique called prospective hindsight can add to a fault tree's ability to improve a strategic planning process.

Slower phloem transport in gymnosperm trees can be attributed to higher sieve element resistance.

PubMed

Liesche, Johannes; Windt, Carel; Bohr, Tomas; Schulz, Alexander; Jensen, Kaare H

2015-04-01

In trees, carbohydrates produced in photosynthesizing leaves are transported to roots and other sink organs over distances of up to 100 m inside a specialized transport tissue, the phloem. Angiosperm and gymnosperm trees have a fundamentally different phloem anatomy with respect to cell size, shape and connectivity. Whether these differences have an effect on the physiology of carbohydrate transport, however, is not clear. A meta-analysis of the experimental data on phloem transport speed in trees yielded average speeds of 56 cm h(-1) for angiosperm trees and 22 cm h(-1) for gymnosperm trees. Similar values resulted from theoretical modeling using a simple transport resistance model. Analysis of the model parameters clearly identified sieve element (SE) anatomy as the main factor for the significantly slower carbohydrate transport speed inside the phloem in gymnosperm compared with angiosperm trees. In order to investigate the influence of SE anatomy on the hydraulic resistance, anatomical data on SEs and sieve pores were collected by transmission electron microscopy analysis and from the literature for 18 tree species. Calculations showed that the hydraulic resistance is significantly higher in the gymnosperm than in angiosperm trees. The higher resistance is only partially offset by the considerably longer SEs of gymnosperms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Remote sensing survey of Chinese tallow tree in the Toledo Bend Reservoir area, Louisiana and Texas

USGS Publications Warehouse

Ramsey, Elijah W.; Rangoonwala, Amina; Bannister, Terri; Suzuoki, Yukihiro

2013-01-01

We applied Hyperion sensor satellite data acquired by the National Aeronautics and Space Administration’s Earth Observing-1 (EO-1) satellite in conjunction with reconnaissance surveys to map the occurrences of the invasive Chinese tallow tree (Triadica sebifera) in the Toledo Bend Reservoir study area of northwestern Louisiana and northeastern Texas. The rationale for application of high spectral resolution EO-1 Hyperion data was based on the successful use of Hyperion data in the mapping of Chinese tallow tree in southwestern Louisiana in 2005. In contrast to the single Hyperion image used in the 2005 project, more than 20 EO-1 Hyperion and Advanced Land Imager (ALI) images of the study area were collected in 2009 and 2010 during the fall senescence when Chinese tallow tree leaves turn red. Atmospherically corrected reflectance spectra of Hyperion imagery collected at ground and aerial observation locations provided the input datasets used in the program for spectral discrimination analysis. Discrimination analysis was used to identify spectral indicator sets to best explain variance contained in the input databases. The expectation was that at least one set of Hyperion-based indicator spectra would uniquely identify occurrences of red-leaf Chinese tallow tree; however, no combination of Hyperion-based reflectance datasets produced a unique identifier. The inability to discover a unique spectral indicator resulted primarily from relatively sparse coverage by red-leaf Chinese tallow tree within the study area (percentage of coverage was less than 5 percent per 30- by 30-meter Hyperion pixel). To enhance the performance of the spectral discrimination analysis, leaf and canopy spectra of Chinese tallow tree were added to the input datasets to guide the indicator selection. In addition, input databases were segregated by land class obtained from an ALI-based landcover classification in order to reduce the input variance and to promote spectral discrimination of red-leaf Chinese tallow tree. Although no unique spectral identifier for red-leaf Chinese tallow tree was uncovered with these enhanced methods, in some cases predicted spatial patterns throughout the Hyperion images revealed alignment with vegetation associations within each land class that was often observed to contain Chinese tallow trees. These instances were associated particularly with the addition of helicopter-based spectra to the input databases. It was attempted to extend such predictions of likely occurrences of Chinese tallow tree by mapping six of the nine Hyperion swaths and four of the nine land classes, but this attempt produced uncertain results that could not be fully evaluated for accuracy. Even though the final mapping showed promise in identifying likely Chinese tallow tree occurrences, the low percentage of occurrences hindered mapping performance and validation. Results of the mapping suggested that successful detection of Chinese tallow tree in the study area would require a spectral sensor similar to the Hyperion but with a higher ground-level spatial resolution. Although the Hyperion-based spectral mapping did not provide the desired results, the associated field (ground and aerial) surveys did provide for a qualitative assessment of the overall Chinese tallow tree distribution within the study area. Ground and aerial surveys suggested that Chinese tallow tree occurrences were uncommon and were without an observed pattern in relation to proximity to the Toledo Bend Reservoir. Although uncommon and scattered, Chinese tallow trees and shrubs most commonly existed along forest edges, water edges, and fence lines, probably most in line with seed dispersal by birds. Chinese tallow trees were observed to be more densely dispersed within some scrublands and grasslands than were observed in pine, hardwood, and mixed forests.

Are Temperate Canopy Spiders Tree-Species Specific?

PubMed Central

Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

2014-01-01

Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood. PMID:24586251

Are temperate canopy spiders tree-species specific?

PubMed

Mupepele, Anne-Christine; Müller, Tobias; Dittrich, Marcus; Floren, Andreas

2014-01-01

Arboreal spiders in deciduous and coniferous trees were investigated on their distribution and diversity. Insecticidal knock-down was used to comprehensively sample spiders from 175 trees from 2001 to 2003 in the Białowieża forest and three remote forests in Poland. We identified 140 species from 9273 adult spiders. Spider communities were distinguished between deciduous and coniferous trees. The richest fauna was collected from Quercus where beta diversity was also highest. A tree-species-specific pattern was clearly observed for Alnus, Carpinus, Picea and Pinus trees and also for those tree species that were fogged in only four or three replicates, namely Betula and Populus. This hitherto unrecognised association was mainly due to the community composition of common species identified in a Dufrene-Legendre indicator species analysis. It was not caused by spatial or temporal autocorrelation. Explaining tree-species specificity for generalist predators like spiders is difficult and has to involve physical and ecological tree parameters like linkage with the abundance of prey species. However, neither did we find a consistent correlation of prey group abundances with spiders nor could differences in spider guild composition explain the observed pattern. Our results hint towards the importance of deterministic mechanisms structuring communities of generalist canopy spiders although the casual relationship is not yet understood.

Tree Islands of the Florida Everglades - A Disappearing Resource

USGS Publications Warehouse

,

2003-01-01

Until recently, the timing and cause of tree island formation have been poorly understood, with estimates of initial tree-island development as early as thousands of years ago to as recently as the last few decades. To increase our knowledge about the origins of these features, sediment cores were collected on and around tree islands. These cores were dated using radioisotopic techniques, including carbon-14 dating, which provides reliable dates from ~40,000 to ~300 years ago, and lead-210 dating, which provides age models for the last century. These age models were paired with vegetational reconstruction based on pollen analysis from cores to identify the timing of tree-island formation and assess past tree-island response to hydrologic changes in the 20th century.

Using decision tree analysis to identify risk factors for relapse to smoking

PubMed Central

Piper, Megan E.; Loh, Wei-Yin; Smith, Stevens S.; Japuntich, Sandra J.; Baker, Timothy B.

2010-01-01

This research used classification tree analysis and logistic regression models to identify risk factors related to short- and long-term abstinence. Baseline and cessation outcome data from two smoking cessation trials, conducted from 2001 to 2002, in two Midwestern urban areas, were analyzed. There were 928 participants (53.1% women, 81.8% white) with complete data. Both analyses suggest that relapse risk is produced by interactions of risk factors and that early and late cessation outcomes reflect different vulnerability factors. The results illustrate the dynamic nature of relapse risk and suggest the importance of efficient modeling of interactions in relapse prediction. PMID:20397871

Fragment-based prediction of skin sensitization using recursive partitioning

NASA Astrophysics Data System (ADS)

Lu, Jing; Zheng, Mingyue; Wang, Yong; Shen, Qiancheng; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

2011-09-01

Skin sensitization is an important toxic endpoint in the risk assessment of chemicals. In this paper, structure-activity relationships analysis was performed on the skin sensitization potential of 357 compounds with local lymph node assay data. Structural fragments were extracted by GASTON (GrAph/Sequence/Tree extractiON) from the training set. Eight fragments with accuracy significantly higher than 0.73 ( p < 0.1) were retained to make up an indicator descriptor fragment. The fragment descriptor and eight other physicochemical descriptors closely related to the endpoint were calculated to construct the recursive partitioning tree (RP tree) for classification. The balanced accuracy of the training set, test set I, and test set II in the leave-one-out model were 0.846, 0.800, and 0.809, respectively. The results highlight that fragment-based RP tree is a preferable method for identifying skin sensitizers. Moreover, the selected fragments provide useful structural information for exploring sensitization mechanisms, and RP tree creates a graphic tree to identify the most important properties associated with skin sensitization. They can provide some guidance for designing of drugs with lower sensitization level.

Boreal tree hydrodynamics: asynchronous, diverging, yet complementary.

PubMed

Pappas, Christoforos; Matheny, Ashley M; Baltzer, Jennifer L; Barr, Alan G; Black, T Andrew; Bohrer, Gil; Detto, Matteo; Maillet, Jason; Roy, Alexandre; Sonnentag, Oliver; Stephens, Jilmarie

2018-05-08

Water stress has been identified as a key mechanism of the contemporary increase in tree mortality rates in northwestern North America. However, a detailed analysis of boreal tree hydrodynamics and their interspecific differences is still lacking. Here we examine the hydraulic behaviour of co-occurring larch (Larix laricina) and black spruce (Picea mariana), two characteristic boreal tree species, near the southern limit of the boreal ecozone in central Canada. Sap flux density (Js), concurrently recorded stem radius fluctuations and meteorological conditions are used to quantify tree hydraulic functioning and to scrutinize tree water-use strategies. Our analysis revealed asynchrony in the diel hydrodynamics of the two species with the initial rise in Js occurring 2 h earlier in larch than in black spruce. Interspecific differences in larch and black spruce crown architecture explained the observed asynchrony in their hydraulic functioning. Furthermore, the two species exhibited diverging stomatal regulation strategies with larch and black spruce employing relatively isohydric and anisohydric behaviour, respectively. Such asynchronous and diverging tree-level hydrodynamics provide new insights into the ecosystem-level complementarity in tree form and function, with implications for understanding boreal forests' water and carbon dynamics and their resilience to environmental stress.

Characterization of bacterial knot disease caused by Pseudomonas savastanoi pv. savastanoi on pomegranate (Punica granatum L.) trees: a new host of the pathogen.

PubMed

Bozkurt, I A; Soylu, S; Mirik, M; Ulubas Serce, C; Baysal, Ö

2014-11-01

This study aimed to isolate and identify the causal organism causing hyperplastic outgrowths (knots) on stems and branches of pomegranate trees in the Eastern Mediterranean region of Turkey. Bacterial colonies were isolated from young knots on plates containing selective nutrient media. Biochemical tests, fatty acid analysis and PCR were performed to identify possible causal disease agent. Representative isolates were identified as Pseudomonas.pv.savastanoi (Psv) using biochemical tests, fatty acid profiling and PCR. Following inoculation of pomegranate plants (cv. hicaz) with bacterial suspensions, 25 of 54 bacterial isolates caused typical knots at the site of inoculation. PCR analysis, using specific primer for Psv, generated a single amplicon from all isolates. The similarity of the sequence of Turkish pomegranate isolate was 99% similar to the corresponding gene sequences of Psv in the databases. Based on symptoms, biochemical, molecular, pathogenicity tests and sequence analyses, the disease agent of knots observed on the pomegranate trees is Psv. To the best of our knowledge, this research has revealed pomegranate as a natural host of Psv, which extends the list of host plant species affected by the pathogen in the world and Turkey. Pomegranate trees were affected by the disease with outgrowths (galls or knot) disease. Currently, there is no published study on disease agent(s) causing the galls or knots on pomegranate trees in worldwide. Bacterial colonies were isolated from young knots. The causal agent of the knot Pseudomonas savastanoi pv.savastanoi (Psv) was identified based on symptoms, biochemical, molecular methods, pathogenicity tests and sequence analysis. To the best of our knowledge, this is the first report of Psv on pomegranate as a natural host, which extends the growing list of plant species affected by this bacterium in the world and Turkey. © 2014 The Society for Applied Microbiology.

Predictability of the future development of aggressive behavior of cranial dural arteriovenous fistulas based on decision tree analysis.

PubMed

Satomi, Junichiro; Ghaibeh, A Ammar; Moriguchi, Hiroki; Nagahiro, Shinji

2015-07-01

The severity of clinical signs and symptoms of cranial dural arteriovenous fistulas (DAVFs) are well correlated with their pattern of venous drainage. Although the presence of cortical venous drainage can be considered a potential predictor of aggressive DAVF behaviors, such as intracranial hemorrhage or progressive neurological deficits due to venous congestion, accurate statistical analyses are currently not available. Using a decision tree data mining method, the authors aimed at clarifying the predictability of the future development of aggressive behaviors of DAVF and at identifying the main causative factors. Of 266 DAVF patients, 89 were eligible for analysis. Under observational management, 51 patients presented with intracranial hemorrhage/infarction during the follow-up period. The authors created a decision tree able to assess the risk for the development of aggressive DAVF behavior. Evaluated by 10-fold cross-validation, the decision tree's accuracy, sensitivity, and specificity were 85.28%, 88.33%, and 80.83%, respectively. The tree shows that the main factor in symptomatic patients was the presence of cortical venous drainage. In its absence, the lesion location determined the risk of a DAVF developing aggressive behavior. Decision tree analysis accurately predicts the future development of aggressive DAVF behavior.

Poster - Thur Eve - 05: Safety systems and failure modes and effects analysis for a magnetic resonance image guided radiation therapy system.

PubMed

Lamey, M; Carlone, M; Alasti, H; Bissonnette, J P; Borg, J; Breen, S; Coolens, C; Heaton, R; Islam, M; van Proojen, M; Sharpe, M; Stanescu, T; Jaffray, D

2012-07-01

An online Magnetic Resonance guided Radiation Therapy (MRgRT) system is under development. The system is comprised of an MRI with the capability of travel between and into HDR brachytherapy and external beam radiation therapy vaults. The system will provide on-line MR images immediately prior to radiation therapy. The MR images will be registered to a planning image and used for image guidance. With the intention of system safety we have performed a failure modes and effects analysis. A process tree of the facility function was developed. Using the process tree as well as an initial design of the facility as guidelines possible failure modes were identified, for each of these failure modes root causes were identified. For each possible failure the assignment of severity, detectability and occurrence scores was performed. Finally suggestions were developed to reduce the possibility of an event. The process tree consists of nine main inputs and each of these main inputs consisted of 5 - 10 sub inputs and tertiary inputs were also defined. The process tree ensures that the overall safety of the system has been considered. Several possible failure modes were identified and were relevant to the design, construction, commissioning and operating phases of the facility. The utility of the analysis can be seen in that it has spawned projects prior to installation and has lead to suggestions in the design of the facility. © 2012 American Association of Physicists in Medicine.

Risk Analysis Methods for Deepwater Port Oil Transfer Systems

DOT National Transportation Integrated Search

1976-06-01

This report deals with the risk analysis methodology for oil spills from the oil transfer systems in deepwater ports. Failure mode and effect analysis in combination with fault tree analysis are identified as the methods best suited for the assessmen...

Assessment of tree response to drought: validation of a methodology to identify and test proxies for monitoring past environmental changes in trees.

PubMed

Tene, A; Tobin, B; Dyckmans, J; Ray, D; Black, K; Nieuwenhuis, M

2011-03-01

A thinning experiment stand at Avoca, Ballinvalley, on the east coast of the Republic of Ireland was used to test a developed methodology aimed at monitoring drought stress, based on the analysis of growth rings obtained by coring. The stand incorporated six plots representing three thinning regimes (light, moderate and heavy) and was planted in the spring of 1943 on a brown earth soil. Radial growth (early- and latewood) was measured for the purpose of this study. A multidisciplinary approach was used to assess historic tree response to climate: specifically, the application of statistical tools such as principal component and canonical correlation analysis to dendrochronology, stable isotopes, ring density proxy, blue reflectance and forest biometrics. Results showed that radial growth was a good proxy for monitoring changes to moisture deficit, while maximum density and blue reflectance were appropriate for assessing changes in accumulated temperature for the growing season. Rainfall also influenced radial growth changes but not significantly, and was a major factor in stable carbon and oxygen discrimination, mostly in the latewood formation phase. Stable oxygen isotope analysis was more accurate than radial growth analysis in drought detection, as it helped detect drought signals in both early- and latewood while radial growth analysis only detected the drought signal in earlywood. Many studies have shown that tree rings provide vital information for marking past climatic events. This work provides a methodology to better identify and understand how commonly measured tree proxies relate to environmental parameters, and can best be used to characterize and pinpoint drought events (variously described using parameters such as like moisture deficit, accumulated temperature, rainfall and potential evaporation).

Interim reliability evaluation program, Browns Ferry 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mays, S.E.; Poloski, J.P.; Sullivan, W.H.

1981-01-01

Probabilistic risk analysis techniques, i.e., event tree and fault tree analysis, were utilized to provide a risk assessment of the Browns Ferry Nuclear Plant Unit 1. Browns Ferry 1 is a General Electric boiling water reactor of the BWR 4 product line with a Mark 1 (drywell and torus) containment. Within the guidelines of the IREP Procedure and Schedule Guide, dominant accident sequences that contribute to public health and safety risks were identified and grouped according to release categories.

FBI fingerprint identification automation study: AIDS 3 evaluation report. Volume 7: Top down functional analysis

NASA Technical Reports Server (NTRS)

Mulhall, B. D. L.

1980-01-01

The functions are identified and described in chart form as a tree in which the basic functions, to 'Provide National Identification Service,' are shown at the top. The lower levels of the tree branch out to indicate functions and sub-functions. Symbols are used to indicate whether or not a function was automated in the AIDS 1 or 2 system or is planned to be automated in the AIDS 3 system. The tree chart is shown in detail.

TESTING TREE-CLASSIFIER VARIANTS AND ALTERNATE MODELING METHODOLOGIES IN THE EAST GREAT BASIN MAPPING UNIT OF THE SOUTHWEST REGIONAL GAP ANALYSIS PROJECT (SW REGAP)

EPA Science Inventory

We tested two methods for dataset generation and model construction, and three tree-classifier variants to identify the most parsimonious and thematically accurate mapping methodology for the SW ReGAP project. Competing methodologies were tested in the East Great Basin mapping un...

Parallel peak pruning for scalable SMP contour tree computation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carr, Hamish A.; Weber, Gunther H.; Sewell, Christopher M.

As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this formmore » of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.« less

Characterization of apple stem grooving virus and apple chlorotic leaf spot virus identified in a crab apple tree.

PubMed

Li, Yongqiang; Deng, Congliang; Bian, Yong; Zhao, Xiaoli; Zhou, Qi

2017-04-01

Apple stem grooving virus (ASGV), apple chlorotic leaf spot virus (ACLSV), and prunus necrotic ringspot virus (PNRSV) were identified in a crab apple tree by small RNA deep sequencing. The complete genome sequence of ACLSV isolate BJ (ACLSV-BJ) was 7554 nucleotides and shared 67.0%-83.0% nucleotide sequence identity with other ACLSV isolates. A phylogenetic tree based on the complete genome sequence of all available ACLSV isolates showed that ACLSV-BJ clustered with the isolates SY01 from hawthorn, MO5 from apple, and JB, KMS and YH from pear. The complete nucleotide sequence of ASGV-BJ was 6509 nucleotides (nt) long and shared 78.2%-80.7% nucleotide sequence identity with other isolates. ASGV-BJ and the isolate ASGV_kfp clustered together in the phylogenetic tree as an independent clade. Recombination analysis showed that isolate ASGV-BJ was a naturally occurring recombinant.

A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

PubMed Central

Keremane, Manjunath L.; Lee, Richard F.; Maureira-Butler, Ivan J.; Roose, Mikeal L.

2013-01-01

Background Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species. Methodology and Principal Findings (1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test. Conclusions We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus. PMID:23874615

Mapping and characterizing selected canopy tree species at the Angkor World Heritage site in Cambodia using aerial data.

PubMed

Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

2015-01-01

At present, there is very limited information on the ecology, distribution, and structure of Cambodia's tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman's rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables.

Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data

PubMed Central

Singh, Minerva; Evans, Damian; Tan, Boun Suy; Nin, Chan Samean

2015-01-01

At present, there is very limited information on the ecology, distribution, and structure of Cambodia’s tree species to warrant suitable conservation measures. The aim of this study was to assess various methods of analysis of aerial imagery for characterization of the forest mensuration variables (i.e., tree height and crown width) of selected tree species found in the forested region around the temples of Angkor Thom, Cambodia. Object-based image analysis (OBIA) was used (using multiresolution segmentation) to delineate individual tree crowns from very-high-resolution (VHR) aerial imagery and light detection and ranging (LiDAR) data. Crown width and tree height values that were extracted using multiresolution segmentation showed a high level of congruence with field-measured values of the trees (Spearman’s rho 0.782 and 0.589, respectively). Individual tree crowns that were delineated from aerial imagery using multiresolution segmentation had a high level of segmentation accuracy (69.22%), whereas tree crowns delineated using watershed segmentation underestimated the field-measured tree crown widths. Both spectral angle mapper (SAM) and maximum likelihood (ML) classifications were applied to the aerial imagery for mapping of selected tree species. The latter was found to be more suitable for tree species classification. Individual tree species were identified with high accuracy. Inclusion of textural information further improved species identification, albeit marginally. Our findings suggest that VHR aerial imagery, in conjunction with OBIA-based segmentation methods (such as multiresolution segmentation) and supervised classification techniques are useful for tree species mapping and for studies of the forest mensuration variables. PMID:25902148

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling.

PubMed

Hird, Sarah; Kubatko, Laura; Carstens, Bryan

2010-11-01

We describe a method for estimating species trees that relies on replicated subsampling of large data matrices. One application of this method is phylogeographic research, which has long depended on large datasets that sample intensively from the geographic range of the focal species; these datasets allow systematicists to identify cryptic diversity and understand how contemporary and historical landscape forces influence genetic diversity. However, analyzing any large dataset can be computationally difficult, particularly when newly developed methods for species tree estimation are used. Here we explore the use of replicated subsampling, a potential solution to the problem posed by large datasets, with both a simulation study and an empirical analysis. In the simulations, we sample different numbers of alleles and loci, estimate species trees using STEM, and compare the estimated to the actual species tree. Our results indicate that subsampling three alleles per species for eight loci nearly always results in an accurate species tree topology, even in cases where the species tree was characterized by extremely rapid divergence. Even more modest subsampling effort, for example one allele per species and two loci, was more likely than not (>50%) to identify the correct species tree topology, indicating that in nearly all cases, computing the majority-rule consensus tree from replicated subsampling provides a good estimate of topology. These results were supported by estimating the correct species tree topology and reasonable branch lengths for an empirical 10-locus great ape dataset. Copyright © 2010 Elsevier Inc. All rights reserved.

14 CFR 417.309 - Flight safety system analysis.

Code of Federal Regulations, 2012 CFR

2012-01-01

... system anomaly occurring and all of its effects as determined by the single failure point analysis and... termination system. (c) Single failure point. A command control system must undergo an analysis that... fault tree analysis or a failure modes effects and criticality analysis; (2) Identify all possible...

14 CFR 417.309 - Flight safety system analysis.

Code of Federal Regulations, 2010 CFR

2010-01-01

... system anomaly occurring and all of its effects as determined by the single failure point analysis and... termination system. (c) Single failure point. A command control system must undergo an analysis that... fault tree analysis or a failure modes effects and criticality analysis; (2) Identify all possible...

14 CFR 417.309 - Flight safety system analysis.

Code of Federal Regulations, 2013 CFR

2013-01-01

... system anomaly occurring and all of its effects as determined by the single failure point analysis and... termination system. (c) Single failure point. A command control system must undergo an analysis that... fault tree analysis or a failure modes effects and criticality analysis; (2) Identify all possible...

14 CFR 417.309 - Flight safety system analysis.

Code of Federal Regulations, 2014 CFR

2014-01-01

... system anomaly occurring and all of its effects as determined by the single failure point analysis and... termination system. (c) Single failure point. A command control system must undergo an analysis that... fault tree analysis or a failure modes effects and criticality analysis; (2) Identify all possible...

14 CFR 417.309 - Flight safety system analysis.

Code of Federal Regulations, 2011 CFR

2011-01-01

... system anomaly occurring and all of its effects as determined by the single failure point analysis and... termination system. (c) Single failure point. A command control system must undergo an analysis that... fault tree analysis or a failure modes effects and criticality analysis; (2) Identify all possible...

Climate signal detected in sub-fossil and living oak trees data. An analysis of signal frequency components

NASA Astrophysics Data System (ADS)

Constantin, Nechita; Francisca, Chiriloaei; Maria, Radoane; Ionel, Popa; Nicoae, Radoane

2016-04-01

This study is focused on analysis the frequency components of the signal detected in living and sub-fossil tree ring series from different time periods. The investigation is oriented to analyze signal frequency components (low and high) of the two categories of trees. The interpretation technique of tree ring width is the instrument most often used to elaborate past climatic reconstructions. The annual resolution, but also, the high capacity of trees to accumulate climatic information are attributes which confer to palaeo-environmental reconstructions the biggest credibility. The main objective of the study refers to the evaluation of climatic signal characteristics, both present day climate and palaeo-climate (last 7000 years BP). Modern dendrochronological methods were applied on 350 samples of sub-fossil trees and 400 living trees. The subfossil trunks were sampled from different fluvial environments (Siret, Suceava, Moldova). Their age was determined using radiocarbon, varying from under 100 years to almost 7000 years BP. The subfossil tree species investigated were Quercus, Alnus, Ulmus. Considering living trees, these were identified on eastern part of Romania, in different actual physico-geographical conditions. The studied living tree species consisted in Quercus species (robur and petraea). Each site was investigated regarding stress factors of the sampled tree. The working methods were applied to the total wood series, both late and early, to detect intra-annual level climate information. Each series has been tested to separate individual trees with climatic signal of other trees with different signals (noises determined by competition between individuals or site stress, or anthropic impact). Comparing dendrochronological series (sub-fossil and living trees) we want to identify what significant causes determined the difference in the signal frequencies. Especially, the human interventions registered in the last 2 centuries will be evaluated by these different types of signal in the tree rings. In order to evaluate this aspect we used time series which were standardized to avoid the non-climatic signal. This type of investigation is the first of its kind to Eastern Europe, an area so large (over 50 000 km2) and a high number of sites and individuals studied (about 1000). The obtained results will help us to understand the palaeo-environment evolution in the last Holocene and when human intervention has been really significant.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

Tracing footprints of environmental events in tree ring chemistry using neutron activation analysis

NASA Astrophysics Data System (ADS)

Sahin, Dagistan

The aim of this study is to identify environmental effects on tree-ring chemistry. It is known that industrial pollution, volcanic eruptions, dust storms, acid rain and similar events can cause substantial changes in soil chemistry. Establishing whether a particular group of trees is sensitive to these changes in soil environment and registers them in the elemental chemistry of contemporary growth rings is the over-riding goal of any Dendrochemistry research. In this study, elemental concentrations were measured in tree-ring samples of absolutely dated eleven modern forest trees, grown in the Mediterranean region, Turkey, collected and dated by the Malcolm and Carolyn Wiener Laboratory for Aegean and Near Eastern Dendrochronology laboratory at Cornell University. Correlations between measured elemental concentrations in the tree-ring samples were analyzed using statistical tests to answer two questions. Does the current concentration of a particular element depend on any other element within the tree? And, are there any elements showing correlated abnormal concentration changes across the majority of the trees? Based on the detailed analysis results, the low mobility of sodium and bromine, positive correlations between calcium, zinc and manganese, positive correlations between trace elements lanthanum, samarium, antimony, and gold within tree-rings were recognized. Moreover, zinc, lanthanum, samarium and bromine showed strong, positive correlations among the trees and were identified as possible environmental signature elements. New Dendrochemistry information found in this study would be also useful in explaining tree physiology and elemental chemistry in Pinus nigra species grown in Turkey. Elemental concentrations in tree-ring samples were measured using Neutron Activation Analysis (NAA) at the Pennsylvania State University Radiation Science and Engineering Center (RSEC). Through this study, advanced methodologies for methodological, computational and experimental NAA were developed to ensure an acceptable accuracy and certainty in the elemental concentration measurements in tree-ring samples. Two independent analysis methods of NAA were used; the well known k-zero method and a novel method developed in this study, called the Multi-isotope Iterative Westcott (MIW) method. The MIW method uses reaction rate probabilities for a group of isotopes, which can be calculated by a neutronic simulation or measured by experimentation, and determines the representative values for the neutron flux and neutron flux characterization parameters based on Westcott convention. Elemental concentration calculations for standard reference material and tree-ring samples were then performed using the MIW and k-zero analysis methods of the NAA and the results were cross verified. In the computational part of this study, a detailed burnup coupled neutronic simulation was developed to analyze real-time neutronic changes in a TRIGA Mark III reactor core, in this study, the Penn State Breazeale Reactor (PSBR) core. To the best of the author`s knowledge, this is the first burnup coupled neutronic simulation with realistic time steps and full fuel temperature profile for a TRIGA reactor using Monte Carlo Utility for Reactor Evolutions (MURE) code and Monte Carlo Neutral-Particle Code (MCNP) coupling. High fidelity and flexibility in the simulation was aimed to replicate the real core operation through the day. This approach resulted in an enhanced accuracy in neutronic representation of the PSBR core with respect to previous neutronic simulation models for the PSBR core. An important contribution was made in the NAA experimentation practices employed in Dendrochemistry studies at the RSEC. Automated laboratory control and analysis software for NAA measurements in the RSEC Radionuclide Applications Laboratory was developed. Detailed laboratory procedures were written in this study comprising preparation, handling and measurements of tree-ring samples in the Radionuclide Applications Laboratory.

treespace: Statistical exploration of landscapes of phylogenetic trees.

PubMed

Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline

2017-11-01

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Transcriptomic Analysis of Leaf in Tree Peony Reveals Differentially Expressed Pigments Genes.

PubMed

Luo, Jianrang; Shi, Qianqian; Niu, Lixin; Zhang, Yanlong

2017-02-20

Tree peony (Paeonia suffruticosa Andrews) is an important traditional flower in China. Besides its beautiful flower, the leaf of tree peony has also good ornamental value owing to its leaf color change in spring. So far, the molecular mechanism of leaf color change in tree peony is unclear. In this study, the pigment level and transcriptome of three different color stages of tree peony leaf were analyzed. The purplish red leaf was rich in anthocyanin, while yellowish green leaf was rich in chlorophyll and carotenoid. Transcriptome analysis revealed that 4302 differentially expressed genes (DEGs) were upregulated, and 4225 were downregulated in the purplish red leaf vs. yellowish green leaf. Among these DEGs, eight genes were predicted to participate in anthocyanin biosynthesis, eight genes were predicted involved in porphyrin and chlorophyll metabolism, and 10 genes were predicted to participate in carotenoid metabolism. In addition, 27 MYBs, 20 bHLHs, 36 WD40 genes were also identified from DEGs. Anthocyanidin synthase (ANS) is the key gene that controls the anthocyanin level in tree peony leaf. Protochlorophyllide oxido-reductase (POR) is the key gene which regulated the chlorophyll content in tree peony leaf.

Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript.

PubMed

Shearman, Jeremy R; Sangsrakru, Duangjai; Ruang-Areerate, Panthita; Sonthirod, Chutima; Uthaipaisanwong, Pichahpuk; Yoocha, Thippawan; Poopear, Supannee; Theerawattanasuk, Kanikar; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

2014-02-10

The rubber tree, Hevea brasiliensis, is an important plant species that is commercially grown to produce latex rubber in many countries. The rubber tree variety BPM 24 exhibits cytoplasmic male sterility, inherited from the variety GT 1. We constructed the rubber tree mitochondrial genome of a cytoplasmic male sterile variety, BPM 24, using 454 sequencing, including 8 kb paired-end libraries, plus Illumina paired-end sequencing. We annotated this mitochondrial genome with the aid of Illumina RNA-seq data and performed comparative analysis. We then compared the sequence of BPM 24 to the contigs of the published rubber tree, variety RRIM 600, and identified a rearrangement that is unique to BPM 24 resulting in a novel transcript containing a portion of atp9. The novel transcript is consistent with changes that cause cytoplasmic male sterility through a slight reduction to ATP production efficiency. The exhaustive nature of the search rules out alternative causes and supports previous findings of novel transcripts causing cytoplasmic male sterility.

Climate Controls on Tree Growth Across Species and Sites in Northeastern Arizona

NASA Astrophysics Data System (ADS)

Schwan, M. R.; Guiterman, C. H.; Anchukaitis, K. J.

2016-12-01

Understanding how forests will respond to ongoing climate change is important for conservation and resource management. Conifer forests in the US Southwest are predicted to be particularly at risk from increased drought and higher temperatures projected to occur in the region. Tree-ring studies shed light on how trees respond to climate, but there remains considerable uncertainty as to which climate factors are most important, and which species are most at risk. Confounding climate and environmental factors, biological differences among species, and biogeography often complicate cross-species analysis. Here we present a multi-species, multivariate analysis of tree growth response to climate variability. We analyze data from three coexisting conifer tree species at two sites near Canyon de Chelly, Arizona. We use a high-resolution PRISM gridded climate dataset to determine the growth responses across species and sites to temperature and precipitation. We identify both common and differential responses in our data and use these to infer possible risks these forest communities may face under a changing climate.

Mines Systems Safety Improvement Using an Integrated Event Tree and Fault Tree Analysis

NASA Astrophysics Data System (ADS)

Kumar, Ranjan; Ghosh, Achyuta Krishna

2017-04-01

Mines systems such as ventilation system, strata support system, flame proof safety equipment, are exposed to dynamic operational conditions such as stress, humidity, dust, temperature, etc., and safety improvement of such systems can be done preferably during planning and design stage. However, the existing safety analysis methods do not handle the accident initiation and progression of mine systems explicitly. To bridge this gap, this paper presents an integrated Event Tree (ET) and Fault Tree (FT) approach for safety analysis and improvement of mine systems design. This approach includes ET and FT modeling coupled with redundancy allocation technique. In this method, a concept of top hazard probability is introduced for identifying system failure probability and redundancy is allocated to the system either at component or system level. A case study on mine methane explosion safety with two initiating events is performed. The results demonstrate that the presented method can reveal the accident scenarios and improve the safety of complex mine systems simultaneously.

Plasticity in dendroclimatic response across the distribution range of Aleppo Pine (Pinus halepensis)

Treesearch

Martin de Luis; Katarina Cufar; Alfredo Di Filippo; Klemen Novak; Andreas Papadopoulos; Gianluca Piovesan; Cyrille B. K. Rathgeber; José Raventós; Miguel Angel Saz; Kevin T. Smith

2013-01-01

We investigated the variability of the climate-growth relationship of Aleppo pine across its distribution range in the Mediterranean Basin. We constructed a network of tree-ring index chronologies from 63 sites across the region. Correlation function analysis identified the relationships of tree-ring index to climate factors for each site. We also estimated the...

Risk Factors of Falls in Community-Dwelling Older Adults: Logistic Regression Tree Analysis

ERIC Educational Resources Information Center

Yamashita, Takashi; Noe, Douglas A.; Bailer, A. John

2012-01-01

Purpose of the Study: A novel logistic regression tree-based method was applied to identify fall risk factors and possible interaction effects of those risk factors. Design and Methods: A nationally representative sample of American older adults aged 65 years and older (N = 9,592) in the Health and Retirement Study 2004 and 2006 modules was used.…

Tree species associations of Pinus echinata mill. over a large-scale sampling regime on the interior highlands of Arkansas

Treesearch

James F., Jr. Rosson

2007-01-01

The Interior Highlands physiographic province of Arkansas is considered the ecological center of the geographic distribution of shortleaf pine (Pinus echinata Mill.). I used data from the U.S. Forest Service, Forest Inventory and Analysis (FIA) program to identify the major tree species associates of P. echinata across this 66,700-...

Propensity score estimation: neural networks, support vector machines, decision trees (CART), and meta-classifiers as alternatives to logistic regression.

PubMed

Westreich, Daniel; Lessler, Justin; Funk, Michele Jonsson

2010-08-01

Propensity scores for the analysis of observational data are typically estimated using logistic regression. Our objective in this review was to assess machine learning alternatives to logistic regression, which may accomplish the same goals but with fewer assumptions or greater accuracy. We identified alternative methods for propensity score estimation and/or classification from the public health, biostatistics, discrete mathematics, and computer science literature, and evaluated these algorithms for applicability to the problem of propensity score estimation, potential advantages over logistic regression, and ease of use. We identified four techniques as alternatives to logistic regression: neural networks, support vector machines, decision trees (classification and regression trees [CART]), and meta-classifiers (in particular, boosting). Although the assumptions of logistic regression are well understood, those assumptions are frequently ignored. All four alternatives have advantages and disadvantages compared with logistic regression. Boosting (meta-classifiers) and, to a lesser extent, decision trees (particularly CART), appear to be most promising for use in the context of propensity score analysis, but extensive simulation studies are needed to establish their utility in practice. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Analysis of polycyclic aromatic hydrocarbons in tree-rings of Masson pine (Pinus massoniana L.) from two industrial sites in the Pearl River Delta, south China.

PubMed

Kuang, Yuan-wen; Zhou, Guo-yi; Wen, Da-zhi; Li, Jiong; Sun, Fang-fang

2011-09-01

Concentrations of polycyclic aromatic hydrocarbons (PAHs) were examined and potential sources of PAHs were identified from the dated tree-rings of Masson pine (Pinus massoniana L.) near two industrial sites (Danshuikeng, DSK and Xiqiaoshan, XQS) in the Pearl River Delta of south China. Total concentrations of PAHs (∑PAHs) were revealed with similar patterns of temporal trends in the tree-rings at both sites, suggesting tree-rings recorded the historical variation in atmospheric PAHs. The differences of individual PAHs and of ∑PAHs detected in the tree-rings between the two sites reflected the historical differences of airborne PAHs. Regional changes in industrial activities might contribute to the site-specific and period-specific patterns of the tree-ring PAHs. The diagnostic PAH ratios of Ant/(Ant + PA), FL/(FL + Pyr), and BaA/(BaA + Chr)) revealed that PAHs in the tree-rings at both sites mainly stemmed from the combustion process (pyrogenic sources). Principal component analysis further confirmed that wood burning, coal combustion, diesel, and gasoline-powered vehicular emissions were the dominant contributors of PAHs sources at DSK, while diesel combustion, gasoline and natural gas combustion, and incomplete coal combustion were responsible for the main origins of PAHs at XQS. Tree-ring analysis of PAHs was indicative of PAHs from a mixture of sources of combustion, thus minimizing the bias of short-term active air sampling.

Cross-reactivity profiles of legumes and tree nuts using the xMAP® multiplex food allergen detection assay.

PubMed

Cho, Chung Y; Oles, Carolyn; Nowatzke, William; Oliver, Kerry; Garber, Eric A E

2017-10-01

The homology between proteins in legumes and tree nuts makes it common for individuals with food allergies to be allergic to multiple legumes and tree nuts. This propensity for allergenic and antigenic cross-reactivity means that commonly employed commercial immunodiagnostic assays (e.g., dipsticks) for the detection of food allergens may not always accurately detect, identify, and quantitate legumes and tree nuts unless additional orthogonal analytical methods or secondary measures of analysis are employed. The xMAP ® Multiplex Food Allergen Detection Assay (FADA) was used to determine the cross-reactivity patterns and the utility of multi-antibody antigenic profiling to distinguish between legumes and tree nuts. Pure legumes and tree nuts extracted using buffered detergent displayed a high level of cross-reactivity that decreased upon dilution or by using a buffer (UD buffer) designed to increase the stringency of binding conditions and reduce the occurrence of false positives due to plant-derived lectins. Testing for unexpected food allergens or the screening for multiple food allergens often involves not knowing the identity of the allergen present, its concentration, or the degree of modification during processing. As such, the analytical response measured may represent multiple antigens of varying antigenicity (cross-reactivity). This problem of multiple potential analytes is usually unresolved and the focus becomes the primary analyte, the antigen the antibody was raised against, or quantitative interpretation of the content of the analytical sample problematic. The alternative solution offered here to this problem is the use of an antigenic profile as generated by the xMAP FADA using multiple antibodies (bead sets). By comparing the antigenic profile to standards, the allergen may be identified along with an estimate of the concentration present. Cluster analysis of the xMAP FADA data was also performed and agreed with the known phylogeny of the legumes and tree nuts being analyzed. Graphical abstract The use of cluster analysis to compare the multi-antigen profiles of food allergens.

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

PubMed

Allman, Elizabeth S; Degnan, James H; Rhodes, John A

2011-06-01

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

Causation mechanism analysis for haze pollution related to vehicle emission in Guangzhou, China by employing the fault tree approach.

PubMed

Huang, Weiqing; Fan, Hongbo; Qiu, Yongfu; Cheng, Zhiyu; Xu, Pingru; Qian, Yu

2016-05-01

Recently, China has frequently experienced large-scale, severe and persistent haze pollution due to surging urbanization and industrialization and a rapid growth in the number of motor vehicles and energy consumption. The vehicle emission due to the consumption of a large number of fossil fuels is no doubt a critical factor of the haze pollution. This work is focused on the causation mechanism of haze pollution related to the vehicle emission for Guangzhou city by employing the Fault Tree Analysis (FTA) method for the first time. With the establishment of the fault tree system of "Haze weather-Vehicle exhausts explosive emission", all of the important risk factors are discussed and identified by using this deductive FTA method. The qualitative and quantitative assessments of the fault tree system are carried out based on the structure, probability and critical importance degree analysis of the risk factors. The study may provide a new simple and effective tool/strategy for the causation mechanism analysis and risk management of haze pollution in China. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dataset for forensic analysis of B-tree file system.

PubMed

Wani, Mohamad Ahtisham; Bhat, Wasim Ahmad

2018-06-01

Since B-tree file system (Btrfs) is set to become de facto standard file system on Linux (and Linux based) operating systems, Btrfs dataset for forensic analysis is of great interest and immense value to forensic community. This article presents a novel dataset for forensic analysis of Btrfs that was collected using a proposed data-recovery procedure. The dataset identifies various generalized and common file system layouts and operations, specific node-balancing mechanisms triggered, logical addresses of various data structures, on-disk records, recovered-data as directory entries and extent data from leaf and internal nodes, and percentage of data recovered.

Spatial Distribution and Site-Specific Spraying of Main Sucking Pests of Elm Trees.

PubMed

Karimzadeh, R; Iranipour, S

2017-06-01

Elm trees are important landscape trees and sucking insects weaken the elm trees and produce large amounts of honeydew. The main objectives of this study were to identify main honeydew-producing pests of elm trees and do site-specific spraying against these pests. To map the spatial distribution of the sucking pests in the large scale, the study area was divided into 40 × 40 m grids and one tree was chosen randomly from each grid (a total of 55 trees). These trees were sampled twice a year in 2011 and 2012. Each sample was a 30-cm branch terminal. Eight samples were taken from each tree in four cardinal directions and two canopy levels. The number of sucking insects and leaves of each sample were counted and recorded. Spatial analysis of the data was carried out using geostatistics. Kriging was used for producing prediction maps. Insecticide application was restricted to the regions with populations higher than threshold. To identify within-tree distribution of the honeydew-producing pests, six and four elm trees were chosen in 2011 and 2012 respectively, and sampled weekly. These trees were sampled as described previously. European elm scale (EES), Gossyparia spuria (Modeer) and two species of aphids were the dominant honeydew-producing pests. The results revealed that the effects of direction, canopy level and their interactions on insect populations were not statistically significant (P < 0.05). Site-specific spraying decreased the amount of insecticides used by ca. 20%, while satisfactory control of the sucking pests and honeydew excretion was obtained. Considering the environmental and economic benefits of site-specific spraying, it is worth doing more complementary works in this area.

Obesity as a risk factor for developing functional limitation among older adults: A conditional inference tree analysis.

PubMed

Cheng, Feon W; Gao, Xiang; Bao, Le; Mitchell, Diane C; Wood, Craig; Sliwinski, Martin J; Smiciklas-Wright, Helen; Still, Christopher D; Rolston, David D K; Jensen, Gordon L

2017-07-01

To examine the risk factors of developing functional decline and make probabilistic predictions by using a tree-based method that allows higher order polynomials and interactions of the risk factors. The conditional inference tree analysis, a data mining approach, was used to construct a risk stratification algorithm for developing functional limitation based on BMI and other potential risk factors for disability in 1,951 older adults without functional limitations at baseline (baseline age 73.1 ± 4.2 y). We also analyzed the data with multivariate stepwise logistic regression and compared the two approaches (e.g., cross-validation). Over a mean of 9.2 ± 1.7 years of follow-up, 221 individuals developed functional limitation. Higher BMI, age, and comorbidity were consistently identified as significant risk factors for functional decline using both methods. Based on these factors, individuals were stratified into four risk groups via the conditional inference tree analysis. Compared to the low-risk group, all other groups had a significantly higher risk of developing functional limitation. The odds ratio comparing two extreme categories was 9.09 (95% confidence interval: 4.68, 17.6). Higher BMI, age, and comorbid disease were consistently identified as significant risk factors for functional decline among older individuals across all approaches and analyses. © 2017 The Obesity Society.

Using a stochastic model and cross-scale analysis to evaluate controls on historical low-severity fire regimes

Treesearch

Maureen C. Kennedy; Donald McKenzie

2010-01-01

Fire-scarred trees provide a deep temporal record of historical fire activity, but identifying the mechanisms therein that controlled landscape fire patterns is not straightforward. We use a spatially correlated metric for fire co-occurrence between pairs of trees (the Sørensen distance variogram), with output from a neutral model for fire history, to infer the...

Dynamics of investor spanning trees around dot-com bubble.

PubMed

Ranganathan, Sindhuja; Kivelä, Mikko; Kanniainen, Juho

2018-01-01

We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles.

Dynamics of investor spanning trees around dot-com bubble

PubMed Central

Kivelä, Mikko; Kanniainen, Juho

2018-01-01

We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles. PMID:29897973

Multi-modal management of acromegaly: a value perspective.

PubMed

Kimmell, Kristopher T; Weil, Robert J; Marko, Nicholas F

2015-10-01

The Acromegaly Consensus Group recently released updated guidelines for medical management of acromegaly patients. We subjected these guidelines to a cost analysis. We conducted a cost analysis of the recommendations based on published efficacy rates as well as publicly available cost data. The results were compared to findings from a previously reported comparative effectiveness analysis of acromegaly treatments. Using decision tree software, two models were created based on the Acromegaly Consensus Group's recommendations and the comparative effectiveness analysis. The decision tree for the Consensus Group's recommendations was subjected to multi-way tornado analysis to identify variables that most impacted the value analysis of the decision tree. The value analysis confirmed the Consensus Group's recommendations of somatostatin analogs as first line therapy for medical management. Our model also demonstrated significant value in using dopamine agonist agents as upfront therapy as well. Sensitivity analysis identified the cost of somatostatin analogs and growth hormone receptor antagonists as having the most significant impact on the cost effectiveness of medical therapies. Our analysis confirmed the value of surgery as first-line therapy for patients with surgically accessible lesions. Surgery provides the greatest value for management of patients with acromegaly. However, in accordance with the Acromegaly Consensus Group's recent recommendations, somatostatin analogs provide the greatest value and should be used as first-line therapy for patients who cannot be managed surgically. At present, the substantial cost is the most significant negative factor in the value of medical therapies for acromegaly.

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

PubMed

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Identification of the chemical components of Saussurea involucrata by high-resolution mass spectrometry and the mass spectral trees similarity filter technique.

PubMed

Jia, Zhixin; Wu, Caisheng; Jin, Hongtao; Zhang, Jinlan

2014-11-15

Saussurea involucrata is a rare traditional Chinese medicine (TCM) that displays anti-fatigue, anti-inflammatory and anti-tumor effects. In this paper, the different chemical components of Saussurea involucrata were characterized and identified over a wide dynamic range by high-performance liquid chromatography coupled with high-resolution hybrid mass spectrometry (HPLC/HRMS/MS(n)) and the mass spectral trees similarity filter (MTSF) technique. The aerial parts of Saussurea involucrata were extracted with 75% ethanol. The partial extract was separated on a chromatography column to concentrate the low-concentration compounds. Mass data were acquired using full-scan mass analysis (resolving power 50,000) with data-dependent incorporation of dynamic exclusion analysis. The identified compounds were used as templates to construct a database of mass spectral trees. Data for the unknown compounds were matched with those templates and matching candidate structures were obtained. The detected compounds were characterized based on matching to candidate structures by the MTSF technique and were further identified by their accurate mass weight, multiple-stage analysis and fragmentation patterns and through comparison with literature data. A total of 38 compounds were identified including 19 flavones, 11 phenylpropanoids and 8 sphingolipids. Among them, 7 flavonoids, 8 phenylpropanoids and 8 sphingolipids were identified for the first time in Saussurea involucrata. HPLC/HRMS/MS(n) combined with MTSF was successfully used to discover and identify the chemical compounds in Saussurea involucrata. The results indicated that this combined technique was extremely useful for the rapid detection and identification of the chemical components in TCMs. Copyright © 2014 John Wiley & Sons, Ltd.

One-year measurements of chloroethenes in tree cores and groundwater at the SAP Mimoň Site, Northern Bohemia.

PubMed

Wittlingerova, Z; Machackova, J; Petruzelkova, A; Trapp, S; Vlk, K; Zima, J

2013-02-01

Chlorinated ethenes (CE) are among the most frequent contaminants of soil and groundwater in the Czech Republic. Because conventional methods of subsurface contamination investigation are costly and technically complicated, attention is directed on alternative and innovative field sampling methods. One promising method is sampling of tree cores (plugs of woody tissue extracted from a host tree). Volatile organic compounds can enter into the trunks and other tissues of trees through their root systems. An analysis of the tree core can thus serve as an indicator of the subsurface contamination. Four areas of interest were chosen at the experimental site with CE groundwater contamination and observed fluctuations in groundwater concentrations. CE concentrations in groundwater and tree cores were observed for a 1-year period. The aim was to determine how the CE concentrations in obtained tree core samples correlate with the level of contamination of groundwater. Other factors which can affect the transfer of contaminants from groundwater to wood were also monitored and evaluated (e.g., tree species and age, level of groundwater table, river flow in the nearby Ploučnice River, seasonal effects, and the effect of the remediation technology operation). Factors that may affect the concentration of CE in wood were identified. The groundwater table level, tree species, and the intensity of transpiration appeared to be the main factors within the framework of the experiment. Obtained values documented that the results of tree core analyses can be used to indicate the presence of CE in the subsurface. The results may also be helpful to identify the best sampling period for tree coring and to learn about the time it takes until tree core concentrations react to changes in groundwater conditions. Interval sampling of tree cores revealed possible preservation of the contaminant in the wood of trees.

Modeling time-to-event (survival) data using classification tree analysis.

PubMed

Linden, Ariel; Yarnold, Paul R

2017-12-01

Time to the occurrence of an event is often studied in health research. Survival analysis differs from other designs in that follow-up times for individuals who do not experience the event by the end of the study (called censored) are accounted for in the analysis. Cox regression is the standard method for analysing censored data, but the assumptions required of these models are easily violated. In this paper, we introduce classification tree analysis (CTA) as a flexible alternative for modelling censored data. Classification tree analysis is a "decision-tree"-like classification model that provides parsimonious, transparent (ie, easy to visually display and interpret) decision rules that maximize predictive accuracy, derives exact P values via permutation tests, and evaluates model cross-generalizability. Using empirical data, we identify all statistically valid, reproducible, longitudinally consistent, and cross-generalizable CTA survival models and then compare their predictive accuracy to estimates derived via Cox regression and an unadjusted naïve model. Model performance is assessed using integrated Brier scores and a comparison between estimated survival curves. The Cox regression model best predicts average incidence of the outcome over time, whereas CTA survival models best predict either relatively high, or low, incidence of the outcome over time. Classification tree analysis survival models offer many advantages over Cox regression, such as explicit maximization of predictive accuracy, parsimony, statistical robustness, and transparency. Therefore, researchers interested in accurate prognoses and clear decision rules should consider developing models using the CTA-survival framework. © 2017 John Wiley & Sons, Ltd.

Progress in Australian dendroclimatology: Identifying growth limiting factors in four climate zones.

PubMed

Haines, Heather A; Olley, Jon M; Kemp, Justine; English, Nathan B

2016-12-01

Dendroclimatology can be used to better understand past climate in regions such as Australia where instrumental and historical climate records are sparse and rarely extend beyond 100years. Here we review 36 Australian dendroclimatic studies which cover the four major climate zones of Australia; temperate, arid, subtropical and tropical. We show that all of these zones contain tree and shrub species which have the potential to provide high quality records of past climate. Despite this potential only four dendroclimatic reconstructions have been published for Australia, one from each of the climate zones: A 3592year temperature record for the SE-temperate zone, a 350year rainfall record for the Western arid zone, a 140year rainfall record for the northern tropics and a 146year rainfall record for SE-subtropics. We report on the spatial distribution of tree-ring studies, the environmental variables identified as limiting tree growth in each study, and identify the key challenges in using tree-ring records for climate reconstruction in Australia. We show that many Australian species have yet to be tested for dendroclimatological potential, and that the application of newer techniques including isotopic analysis, carbon dating, wood density measurements, and anatomical analysis, combined with traditional ring-width measurements should enable more species in each of the climate zones to be used, and long-term climate records to be developed across the entire continent. Copyright © 2016 Elsevier B.V. All rights reserved.

Treetrimmer: a method for phylogenetic dataset size reduction.

PubMed

Maruyama, Shinichiro; Eveleigh, Robert J M; Archibald, John M

2013-04-12

With rapid advances in genome sequencing and bioinformatics, it is now possible to generate phylogenetic trees containing thousands of operational taxonomic units (OTUs) from a wide range of organisms. However, use of rigorous tree-building methods on such large datasets is prohibitive and manual 'pruning' of sequence alignments is time consuming and raises concerns over reproducibility. There is a need for bioinformatic tools with which to objectively carry out such pruning procedures. Here we present 'TreeTrimmer', a bioinformatics procedure that removes unnecessary redundancy in large phylogenetic datasets, alleviating the size effect on more rigorous downstream analyses. The method identifies and removes user-defined 'redundant' sequences, e.g., orthologous sequences from closely related organisms and 'recently' evolved lineage-specific paralogs. Representative OTUs are retained for more rigorous re-analysis. TreeTrimmer reduces the OTU density of phylogenetic trees without sacrificing taxonomic diversity while retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion.

Subterranean termites in urban forestry: tree preference and management.

PubMed

Zorzenon, F J; Campos, A E C

2015-04-01

Urban tree deterioration is a common problem all over the world. Inappropriate plant species choice and inadequate planting may lead to micro and macro organism attacks, such as pests and diseases. Subterranean termite damage is common and may promote tree falls. In order to help urban forestry planning, this work was carried out for 9 years on 1477 street trees in a neighborhood in the city of São Paulo, Brazil. Plants were identified to species, grouped as native, exotic plants, and palm trees, and their measures of circumference at breast height (CBH) were taken, in order to evaluate if subterranean termite damages are related to tree size and plant group. Four subterranean termite species were identified infesting up to 27% of the plants, with Coptotermes gestroi (Wasmann) being the most common. Palm trees were not damaged by subterranean termites, while native plants are the most susceptible, especially Caesalpinia pluviosa var. peltophoroides (Fabaceae). Among the native plants monitored C. pluviosa var. peltophoroides, Caesalpinia ferrea var. leiostachya, Erythrina speciosa, Piptadenia gonoacantha (Fabaceae), Gochnatia polymorpha (Asteraceae), Tibouchina granulosa (Melastomataceae), and Handroanthus spp. (Bignoniaceae), the latter was the least damaged. Exotic plants were also susceptible with the exception of Lagerstroemia indica (Lythraceae) and Platanus acerifolia (Platanaceae). Correlation analysis showed that the higher the CBH value, the higher the percentage of internal damage by C. gestroi. Infested trees were treated with imidacloprid and thiamethoxam, and subterranean termites were effectively controlled during the 9-year study.

Identification of extremely premature infants at high risk of rehospitalization.

PubMed

Ambalavanan, Namasivayam; Carlo, Waldemar A; McDonald, Scott A; Yao, Qing; Das, Abhik; Higgins, Rosemary D

2011-11-01

Extremely low birth weight infants often require rehospitalization during infancy. Our objective was to identify at the time of discharge which extremely low birth weight infants are at higher risk for rehospitalization. Data from extremely low birth weight infants in Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network centers from 2002-2005 were analyzed. The primary outcome was rehospitalization by the 18- to 22-month follow-up, and secondary outcome was rehospitalization for respiratory causes in the first year. Using variables and odds ratios identified by stepwise logistic regression, scoring systems were developed with scores proportional to odds ratios. Classification and regression-tree analysis was performed by recursive partitioning and automatic selection of optimal cutoff points of variables. A total of 3787 infants were evaluated (mean ± SD birth weight: 787 ± 136 g; gestational age: 26 ± 2 weeks; 48% male, 42% black). Forty-five percent of the infants were rehospitalized by 18 to 22 months; 14.7% were rehospitalized for respiratory causes in the first year. Both regression models (area under the curve: 0.63) and classification and regression-tree models (mean misclassification rate: 40%-42%) were moderately accurate. Predictors for the primary outcome by regression were shunt surgery for hydrocephalus, hospital stay of >120 days for pulmonary reasons, necrotizing enterocolitis stage II or higher or spontaneous gastrointestinal perforation, higher fraction of inspired oxygen at 36 weeks, and male gender. By classification and regression-tree analysis, infants with hospital stays of >120 days for pulmonary reasons had a 66% rehospitalization rate compared with 42% without such a stay. The scoring systems and classification and regression-tree analysis models identified infants at higher risk of rehospitalization and might assist planning for care after discharge.

Identification of Extremely Premature Infants at High Risk of Rehospitalization

PubMed Central

Carlo, Waldemar A.; McDonald, Scott A.; Yao, Qing; Das, Abhik; Higgins, Rosemary D.

2011-01-01

OBJECTIVE: Extremely low birth weight infants often require rehospitalization during infancy. Our objective was to identify at the time of discharge which extremely low birth weight infants are at higher risk for rehospitalization. METHODS: Data from extremely low birth weight infants in Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network centers from 2002–2005 were analyzed. The primary outcome was rehospitalization by the 18- to 22-month follow-up, and secondary outcome was rehospitalization for respiratory causes in the first year. Using variables and odds ratios identified by stepwise logistic regression, scoring systems were developed with scores proportional to odds ratios. Classification and regression-tree analysis was performed by recursive partitioning and automatic selection of optimal cutoff points of variables. RESULTS: A total of 3787 infants were evaluated (mean ± SD birth weight: 787 ± 136 g; gestational age: 26 ± 2 weeks; 48% male, 42% black). Forty-five percent of the infants were rehospitalized by 18 to 22 months; 14.7% were rehospitalized for respiratory causes in the first year. Both regression models (area under the curve: 0.63) and classification and regression-tree models (mean misclassification rate: 40%–42%) were moderately accurate. Predictors for the primary outcome by regression were shunt surgery for hydrocephalus, hospital stay of >120 days for pulmonary reasons, necrotizing enterocolitis stage II or higher or spontaneous gastrointestinal perforation, higher fraction of inspired oxygen at 36 weeks, and male gender. By classification and regression-tree analysis, infants with hospital stays of >120 days for pulmonary reasons had a 66% rehospitalization rate compared with 42% without such a stay. CONCLUSIONS: The scoring systems and classification and regression-tree analysis models identified infants at higher risk of rehospitalization and might assist planning for care after discharge. PMID:22007016

Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript

PubMed Central

2014-01-01

Background The rubber tree, Hevea brasiliensis, is an important plant species that is commercially grown to produce latex rubber in many countries. The rubber tree variety BPM 24 exhibits cytoplasmic male sterility, inherited from the variety GT 1. Results We constructed the rubber tree mitochondrial genome of a cytoplasmic male sterile variety, BPM 24, using 454 sequencing, including 8 kb paired-end libraries, plus Illumina paired-end sequencing. We annotated this mitochondrial genome with the aid of Illumina RNA-seq data and performed comparative analysis. We then compared the sequence of BPM 24 to the contigs of the published rubber tree, variety RRIM 600, and identified a rearrangement that is unique to BPM 24 resulting in a novel transcript containing a portion of atp9. Conclusions The novel transcript is consistent with changes that cause cytoplasmic male sterility through a slight reduction to ATP production efficiency. The exhaustive nature of the search rules out alternative causes and supports previous findings of novel transcripts causing cytoplasmic male sterility. PMID:24512148

Industrial and occupational ergonomics in the petrochemical process industry: a regression trees approach.

PubMed

Bevilacqua, M; Ciarapica, F E; Giacchetta, G

2008-07-01

This work is an attempt to apply classification tree methods to data regarding accidents in a medium-sized refinery, so as to identify the important relationships between the variables, which can be considered as decision-making rules when adopting any measures for improvement. The results obtained using the CART (Classification And Regression Trees) method proved to be the most precise and, in general, they are encouraging concerning the use of tree diagrams as preliminary explorative techniques for the assessment of the ergonomic, management and operational parameters which influence high accident risk situations. The Occupational Injury analysis carried out in this paper was planned as a dynamic process and can be repeated systematically. The CART technique, which considers a very wide set of objective and predictive variables, shows new cause-effect correlations in occupational safety which had never been previously described, highlighting possible injury risk groups and supporting decision-making in these areas. The use of classification trees must not, however, be seen as an attempt to supplant other techniques, but as a complementary method which can be integrated into traditional types of analysis.

Tree growth and climate in the Pacific Northwest, North America: a broad-scale analysis of changing growth environments

Treesearch

Whitney L. Albright; David L. Peterson

2013-01-01

Climate change in the 21st century will affect tree growth in the Pacific Northwest region of North America, although complex climate–growth relationships make it difficult to identify how radial growth will respond across different species distributions. We used a novel method to examine potential growth responses to climate change at a broad geographical scale with a...

Tree communities of lowland warm-temperate old-growth and neighboring shelterbelt forests in the Shikoku region of southwestern Japan

Treesearch

Shigeo Kuramoto; Shigenori Oshioka; Takahisa Hirayama; Kaori Sato; Yasumasa Hirata

2007-01-01

We characterized the tree species composition of a 30 ha old-growth and neighboring shelterbelt (reserved buffer strips among conifer plantations) in warm-temperate forests in the Shikoku region of southwestern Japan. Using a two-way indicator species analysis of data from 28 plots, we identified four structural groups in terms of relative basal area. These structural...

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.

PubMed

Kocot, Kevin M; Citarella, Mathew R; Moroz, Leonid L; Halanych, Kenneth M

2013-01-01

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

Floral markers of strawberry tree (Arbutus unedo L.) honey.

PubMed

Tuberoso, Carlo I G; Bifulco, Ersilia; Caboni, Pierluigi; Cottiglia, Filippo; Cabras, Paolo; Floris, Ignazio

2010-01-13

Strawberry tree honey, due to its characteristic bitter taste, is one of the most typical Mediterranean honeys, with Sardinia being one of the largest producers. According to specific chemical studies, homogentisic acid was identified as a possible marker of this honey. This work, based on HPLC-DAD-MS/MS analysis of strawberry tree (Arbutus unedo L.) honeys, previously selected by sensory evaluation and melissopalynological analysis, showed that, in addition to the above-mentioned acid, there were other high levels of substances useful for the botanical classification of this unifloral honey. Two of these compounds were isolated and identified as (+/-)-2-cis,4-trans-abscisic acid (c,t-ABA) and (+/-)-2-trans,4-trans-abscisic acid (t,t-ABA). A third compound, a new natural product named unedone, was characterized as an epoxidic derivative of the above-mentioned acids. Structures of c,t-ABA, t,t-ABA, and unedone were elucidated on the basis of extensive 1D and 2D NMR experiments, as well as HPLC-MS/MS and Q-TOF analysis. In selected honeys the average amounts of c,t-ABA, t,t-ABA, and unedone were 176.2+/-25.4, 162.3+/-21.1, and 32.9+/-7.1 mg/kg, respectively. Analysis of the A. unedo nectar confirmed the floral origin of these compounds found in the honey. Abscisic acids were found in other unifloral honeys but not in such high amount and with a constant ratio of about 1:1. For this reason, besides homogentisic acid, these compounds could be used as complementary markers of strawberry tree honey.

Tree-growth analyses to estimate tree species' drought tolerance.

PubMed

Eilmann, Britta; Rigling, Andreas

2012-02-01

Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species.

Diagnostic classification scheme in Iranian breast cancer patients using a decision tree.

PubMed

Malehi, Amal Saki

2014-01-01

The objective of this study was to determine a diagnostic classification scheme using a decision tree based model. The study was conducted as a retrospective case-control study in Imam Khomeini hospital in Tehran during 2001 to 2009. Data, including demographic and clinical-pathological characteristics, were uniformly collected from 624 females, 312 of them were referred with positive diagnosis of breast cancer (cases) and 312 healthy women (controls). The decision tree was implemented to develop a diagnostic classification scheme using CART 6.0 Software. The AUC (area under curve), was measured as the overall performance of diagnostic classification of the decision tree. Five variables as main risk factors of breast cancer and six subgroups as high risk were identified. The results indicated that increasing age, low age at menarche, single and divorced statues, irregular menarche pattern and family history of breast cancer are the important diagnostic factors in Iranian breast cancer patients. The sensitivity and specificity of the analysis were 66% and 86.9% respectively. The high AUC (0.82) also showed an excellent classification and diagnostic performance of the model. Decision tree based model appears to be suitable for identifying risk factors and high or low risk subgroups. It can also assists clinicians in making a decision, since it can identify underlying prognostic relationships and understanding the model is very explicit.

Mapping the Delivery of Societal Benefit through the International Arctic Observations Assessment Framework

NASA Astrophysics Data System (ADS)

Lev, S. M.; Gallo, J.

2017-12-01

The international Arctic scientific community has identified the need for a sustained and integrated portfolio of pan-Arctic Earth-observing systems. In 2017, an international effort was undertaken to develop the first ever Value Tree framework for identifying common research and operational objectives that rely on Earth observation data derived from Earth-observing systems, sensors, surveys, networks, models, and databases to deliver societal benefits in the Arctic. A Value Tree Analysis is a common tool used to support decision making processes and is useful for defining concepts, identifying objectives, and creating a hierarchical framework of objectives. A multi-level societal benefit area value tree establishes the connection from societal benefits to the set of observation inputs that contribute to delivering those benefits. A Value Tree that relies on expert domain knowledge from Arctic and non-Arctic nations, international researchers, Indigenous knowledge holders, and other experts to develop a framework to serve as a logical and interdependent decision support tool will be presented. Value tree examples that map the contribution of Earth observations in the Arctic to achieving societal benefits will be presented in the context of the 2017 International Arctic Observations Assessment Framework. These case studies will highlight specific observing products and capability groups where investment is needed to contribute to the development of a sustained portfolio of Arctic observing systems.

The ability of adults and children to visually identify peanuts and tree nuts.

PubMed

Hostetler, Todd L; Hostetler, Sarah G; Phillips, Gary; Martin, Bryan L

2012-01-01

Peanuts and tree nuts are common food allergens and are the leading cause of fatalities from food-induced anaphylaxis. Dietary avoidance is the primary management of these allergies and requires the ability to identify peanuts or tree nuts. To investigate the ability of adults and children to visually identify peanuts and tree nuts. A nut display was assembled that held peanuts and 9 tree nuts in a total of 19 different forms. Persons 6 years or older completed a worksheet to name the items. One-thousand one-hundred five subjects completed the study. The mean number of peanuts and tree nuts identified by all subjects was 8.4 (44.2%) out of a possible 19. The mean for children ages 6 to 18 was 4.6 (24.2%), compared with 11.1 (58.4%) for adults older than 18 (P < .001). The most commonly identified items were peanut in the shell and without the shell. The least identified was hazelnut (filbert) in the shell and without the shell. No difference was seen in the performance of peanut- or tree nut-allergic subjects compared with nonallergic subjects. Fifty percent of subjects with a peanut or tree nut allergy correctly identified all forms of peanuts or tree nuts to which they are allergic. Parents of peanut- or tree nut-allergic children did no better than parents of children without such allergy. Overall, both children and adults are unreliable at visually identifying most nuts. Treatment of nut allergies with dietary avoidance should include education for both adults and children on identification of peanuts and tree nuts. Copyright © 2012 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality

PubMed Central

Vergara, Pablo M.; Soto, Gerardo E.; Rodewald, Amanda D.; Meneses, Luis O.; Pérez-Hernández, Christian G.

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox’s proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales. PMID:27416115

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality.

PubMed

Vergara, Pablo M; Soto, Gerardo E; Moreira-Arce, Darío; Rodewald, Amanda D; Meneses, Luis O; Pérez-Hernández, Christian G

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox's proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

PubMed

Jensen, Philip J; Fazio, Gennaro; Altman, Naomi; Praul, Craig; McNellis, Timothy W

2014-04-04

Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Gene expression profiling and trait-associated transcript analysis using an apple F1 population readily identified genes physically linked to powdery mildew disease resistance and woolly apple aphid resistance loci. This result was especially useful in apple, where extreme levels of heterozygosity make the development of reliable DNA markers quite difficult. The results suggest that this approach could prove effective in crops with complicated genetics, or for which few genomic information resources are available.

Mapping trees outside forests using high-resolution aerial imagery: a comparison of pixel- and object-based classification approaches.

PubMed

Meneguzzo, Dacia M; Liknes, Greg C; Nelson, Mark D

2013-08-01

Discrete trees and small groups of trees in nonforest settings are considered an essential resource around the world and are collectively referred to as trees outside forests (ToF). ToF provide important functions across the landscape, such as protecting soil and water resources, providing wildlife habitat, and improving farmstead energy efficiency and aesthetics. Despite the significance of ToF, forest and other natural resource inventory programs and geospatial land cover datasets that are available at a national scale do not include comprehensive information regarding ToF in the United States. Additional ground-based data collection and acquisition of specialized imagery to inventory these resources are expensive alternatives. As a potential solution, we identified two remote sensing-based approaches that use free high-resolution aerial imagery from the National Agriculture Imagery Program (NAIP) to map all tree cover in an agriculturally dominant landscape. We compared the results obtained using an unsupervised per-pixel classifier (independent component analysis-[ICA]) and an object-based image analysis (OBIA) procedure in Steele County, Minnesota, USA. Three types of accuracy assessments were used to evaluate how each method performed in terms of: (1) producing a county-level estimate of total tree-covered area, (2) correctly locating tree cover on the ground, and (3) how tree cover patch metrics computed from the classified outputs compared to those delineated by a human photo interpreter. Both approaches were found to be viable for mapping tree cover over a broad spatial extent and could serve to supplement ground-based inventory data. The ICA approach produced an estimate of total tree cover more similar to the photo-interpreted result, but the output from the OBIA method was more realistic in terms of describing the actual observed spatial pattern of tree cover.

Analytical simulation and PROFAT II: a new methodology and a computer automated tool for fault tree analysis in chemical process industries.

PubMed

Khan, F I; Abbasi, S A

2000-07-10

Fault tree analysis (FTA) is based on constructing a hypothetical tree of base events (initiating events) branching into numerous other sub-events, propagating the fault and eventually leading to the top event (accident). It has been a powerful technique used traditionally in identifying hazards in nuclear installations and power industries. As the systematic articulation of the fault tree is associated with assigning probabilities to each fault, the exercise is also sometimes called probabilistic risk assessment. But powerful as this technique is, it is also very cumbersome and costly, limiting its area of application. We have developed a new algorithm based on analytical simulation (named as AS-II), which makes the application of FTA simpler, quicker, and cheaper; thus opening up the possibility of its wider use in risk assessment in chemical process industries. Based on the methodology we have developed a computer-automated tool. The details are presented in this paper.

Decision trees in epidemiological research.

PubMed

Venkatasubramaniam, Ashwini; Wolfson, Julian; Mitchell, Nathan; Barnes, Timothy; JaKa, Meghan; French, Simone

2017-01-01

In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART) technique and the newer Conditional Inference tree (CTree) technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

Dual impacts of climate change: forest migration and turnover through life history.

PubMed

Zhu, Kai; Woodall, Christopher W; Ghosh, Souparno; Gelfand, Alan E; Clark, James S

2014-01-01

Tree species are predicted to track future climate by shifting their geographic distributions, but climate-mediated migrations are not apparent in a recent continental-scale analysis. To better understand the mechanisms of a possible migration lag, we analyzed relative recruitment patterns by comparing juvenile and adult tree abundances in climate space. One would expect relative recruitment to be higher in cold and dry climates as a result of tree migration with juveniles located further poleward than adults. Alternatively, relative recruitment could be higher in warm and wet climates as a result of higher tree population turnover with increased temperature and precipitation. Using the USDA Forest Service's Forest Inventory and Analysis data at regional scales, we jointly modeled juvenile and adult abundance distributions for 65 tree species in climate space of the eastern United States. We directly compared the optimal climate conditions for juveniles and adults, identified the climates where each species has high relative recruitment, and synthesized relative recruitment patterns across species. Results suggest that for 77% and 83% of the tree species, juveniles have higher optimal temperature and optimal precipitation, respectively, than adults. Across species, the relative recruitment pattern is dominated by relatively more abundant juveniles than adults in warm and wet climates. These different abundance-climate responses through life history are consistent with faster population turnover and inconsistent with the geographic trend of large-scale tree migration. Taken together, this juvenile-adult analysis suggests that tree species might respond to climate change by having faster turnover as dynamics accelerate with longer growing seasons and higher temperatures, before there is evidence of poleward migration at biogeographic scales.

The occurrence of the cicada Cicadatra persica on apple trees, Malus domestica, in Erneh, Syria.

PubMed

Dardar, Marah A; Belal, Hamzeh M R; Basheer, Abedlnabi M

2013-01-01

An infestation of Cicadatra persica KirKaldy (Hemiptera: Cicadidae) on apple trees, Malus domestica Borkhausen (Rosales: Rosaceae), was reported for the first time in the apple fruit orchards of Erneh, Syria. Nymphs, adults, exuvia, and exit holes in the soil were observed. The species was identified as C. persica based on morphological characters. Some biological observations and an acoustic analysis of the male's songs were also achieved.

Accurate airway centerline extraction based on topological thinning using graph-theoretic analysis.

PubMed

Bian, Zijian; Tan, Wenjun; Yang, Jinzhu; Liu, Jiren; Zhao, Dazhe

2014-01-01

The quantitative analysis of the airway tree is of critical importance in the CT-based diagnosis and treatment of popular pulmonary diseases. The extraction of airway centerline is a precursor to identify airway hierarchical structure, measure geometrical parameters, and guide visualized detection. Traditional methods suffer from extra branches and circles due to incomplete segmentation results, which induce false analysis in applications. This paper proposed an automatic and robust centerline extraction method for airway tree. First, the centerline is located based on the topological thinning method; border voxels are deleted symmetrically to preserve topological and geometrical properties iteratively. Second, the structural information is generated using graph-theoretic analysis. Then inaccurate circles are removed with a distance weighting strategy, and extra branches are pruned according to clinical anatomic knowledge. The centerline region without false appendices is eventually determined after the described phases. Experimental results show that the proposed method identifies more than 96% branches and keep consistency across different cases and achieves superior circle-free structure and centrality.

Intrathoracic airway wall detection using graph search and scanner PSF information

NASA Astrophysics Data System (ADS)

Reinhardt, Joseph M.; Park, Wonkyu; Hoffman, Eric A.; Sonka, Milan

1997-05-01

Measurements of the in vivo bronchial tree can be used to assess regional airway physiology. High-resolution CT (HRCT) provides detailed images of the lungs and has been used to evaluate bronchial airway geometry. Such measurements have been sued to assess diseases affecting the airways, such as asthma and cystic fibrosis, to measure airway response to external stimuli, and to evaluate the mechanics of airway collapse in sleep apnea. To routinely use CT imaging in a clinical setting to evaluate the in vivo airway tree, there is a need for an objective, automatic technique for identifying the airway tree in the CT images and measuring airway geometry parameters. Manual or semi-automatic segmentation and measurement of the airway tree from a 3D data set may require several man-hours of work, and the manual approaches suffer from inter-observer and intra- observer variabilities. This paper describes a method for automatic airway tree analysis that combines accurate airway wall location estimation with a technique for optimal airway border smoothing. A fuzzy logic, rule-based system is used to identify the branches of the 3D airway tree in thin-slice HRCT images. Raycasting is combined with a model-based parameter estimation technique to identify the approximate inner and outer airway wall borders in 2D cross-sections through the image data set. Finally, a 2D graph search is used to optimize the estimated airway wall locations and obtain accurate airway borders. We demonstrate this technique using CT images of a plexiglass tube phantom.

Using Fault Trees to Advance Understanding of Diagnostic Errors.

PubMed

Rogith, Deevakar; Iyengar, M Sriram; Singh, Hardeep

2017-11-01

Diagnostic errors annually affect at least 5% of adults in the outpatient setting in the United States. Formal analytic techniques are only infrequently used to understand them, in part because of the complexity of diagnostic processes and clinical work flows involved. In this article, diagnostic errors were modeled using fault tree analysis (FTA), a form of root cause analysis that has been successfully used in other high-complexity, high-risk contexts. How factors contributing to diagnostic errors can be systematically modeled by FTA to inform error understanding and error prevention is demonstrated. A team of three experts reviewed 10 published cases of diagnostic error and constructed fault trees. The fault trees were modeled according to currently available conceptual frameworks characterizing diagnostic error. The 10 trees were then synthesized into a single fault tree to identify common contributing factors and pathways leading to diagnostic error. FTA is a visual, structured, deductive approach that depicts the temporal sequence of events and their interactions in a formal logical hierarchy. The visual FTA enables easier understanding of causative processes and cognitive and system factors, as well as rapid identification of common pathways and interactions in a unified fashion. In addition, it enables calculation of empirical estimates for causative pathways. Thus, fault trees might provide a useful framework for both quantitative and qualitative analysis of diagnostic errors. Future directions include establishing validity and reliability by modeling a wider range of error cases, conducting quantitative evaluations, and undertaking deeper exploration of other FTA capabilities. Copyright © 2017 The Joint Commission. Published by Elsevier Inc. All rights reserved.

An application of the lottery competition model to a montane rainforest community of two canopy trees, ohia (Metrosideros polymorpha) and koa (Acacia koa) on Mauna Loa, Hawaii

USGS Publications Warehouse

Hatfield, J.S.; Link, W.A.; Dawson, D.K.; Lindquist, E.L.

1992-01-01

This rainforest occurs on Mauna Loa at 1500-2000 m elevation. Earthwatch volunteers, studying the habitat of 8 native forest bird species (3 endangered), identified 2382 living canopy trees, and 99 dead trees, on 68 study plots, 400 m2 each. Ohia made up 88% of the canopy; koa was 12%. The two-species lottery competition model, a stochastic model in which coexistence of species results from variation in recruitment and death rates, predicts a quadratic-beta distribution for the proportion of space occupied by one species. A discrete version was fit to the live tree data and a likelihood ratio test (p=0.02) was used to test if the mean death rates were equal. This test was corroborated by a contingency table analysis (p=0.03) based on dead trees. Parameter estimates from the two analyses were similar.

Drug Target Mining and Analysis of the Chinese Tree Shrew for Pharmacological Testing

PubMed Central

Liu, Jie; Lee, Wen-hui; Zhang, Yun

2014-01-01

The discovery of new drugs requires the development of improved animal models for drug testing. The Chinese tree shrew is considered to be a realistic candidate model. To assess the potential of the Chinese tree shrew for pharmacological testing, we performed drug target prediction and analysis on genomic and transcriptomic scales. Using our pipeline, 3,482 proteins were predicted to be drug targets. Of these predicted targets, 446 and 1,049 proteins with the highest rank and total scores, respectively, included homologs of targets for cancer chemotherapy, depression, age-related decline and cardiovascular disease. Based on comparative analyses, more than half of drug target proteins identified from the tree shrew genome were shown to be higher similarity to human targets than in the mouse. Target validation also demonstrated that the constitutive expression of the proteinase-activated receptors of tree shrew platelets is similar to that of human platelets but differs from that of mouse platelets. We developed an effective pipeline and search strategy for drug target prediction and the evaluation of model-based target identification for drug testing. This work provides useful information for future studies of the Chinese tree shrew as a source of novel targets for drug discovery research. PMID:25105297

Tree-ring strontium-90 and cesium-137 as potential indicators of radioactive pollution.

PubMed

Kagawa, Akira; Aoki, Toru; Okada, Naoki; Katayama, Yukio

2002-01-01

To examine whether tree rings can be used to detect or assess local historical 90Sr or 137Cs fallout, such as that resulting from the Hiroshima atomic bomb, radial distribution of 90Sr and 137Cs in trees was examined. We studied a gymnosperm [Japanese cedar, Cryptomeria japonica (L. f.) D. Don] and an angiosperm (Japanese persimmon, Diospyros kaki Thunb.) tree species from the vicinity of the atomic bomb hypocenter, and from other locations in Japan. A significant amount of 137Cs was detected in tree rings formed before 1945, indicating lateral migration of Cs. In contrast, the specific activity of 90Sr in the Hiroshima Japanese cedar showed the highest level in 1945, due to relatively immobile characteristics of Sr compared with Cs. Strontium-90 and Sr analyses in tree rings helped identify and distinguish between residual 90Sr activity from the Hiroshima atomic bomb and the atmospheric nuclear testing. This indicates the possibility of detecting or assessing previous local 90Sr pollution through with treering analysis.

IDHEAS – A NEW APPROACH FOR HUMAN RELIABILITY ANALYSIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

G. W. Parry; J.A Forester; V.N. Dang

2013-09-01

This paper describes a method, IDHEAS (Integrated Decision-Tree Human Event Analysis System) that has been developed jointly by the US NRC and EPRI as an improved approach to Human Reliability Analysis (HRA) that is based on an understanding of the cognitive mechanisms and performance influencing factors (PIFs) that affect operator responses. The paper describes the various elements of the method, namely the performance of a detailed cognitive task analysis that is documented in a crew response tree (CRT), and the development of the associated time-line to identify the critical tasks, i.e. those whose failure results in a human failure eventmore » (HFE), and an approach to quantification that is based on explanations of why the HFE might occur.« less

THE USE OF INTER SIMPLE SEQUENCE REPEATS (ISSR) IN DISTINGUISHING NEIGHBORING DOUGLAS-FIR TREES AS A MEANS TO IDENTIFYING TREE ROOTS WITH ABOVE-GROUND BIOMASS

EPA Science Inventory

We are attempting to identify specific root fragments from soil cores with individual trees. We successfully used Inter Simple Sequence Repeats (ISSR) to distinguish neighboring old-growth Douglas-fir trees from one another, while maintaining identity among each tree's parts. W...

Identifying Risk and Protective Factors in Recidivist Juvenile Offenders: A Decision Tree Approach

PubMed Central

Ortega-Campos, Elena; García-García, Juan; Gil-Fenoy, Maria José; Zaldívar-Basurto, Flor

2016-01-01

Research on juvenile justice aims to identify profiles of risk and protective factors in juvenile offenders. This paper presents a study of profiles of risk factors that influence young offenders toward committing sanctionable antisocial behavior (S-ASB). Decision tree analysis is used as a multivariate approach to the phenomenon of repeated sanctionable antisocial behavior in juvenile offenders in Spain. The study sample was made up of the set of juveniles who were charged in a court case in the Juvenile Court of Almeria (Spain). The period of study of recidivism was two years from the baseline. The object of study is presented, through the implementation of a decision tree. Two profiles of risk and protective factors are found. Risk factors associated with higher rates of recidivism are antisocial peers, age at baseline S-ASB, problems in school and criminality in family members. PMID:27611313

Optical Inspection and Morphological Analysis of Diospyros kaki Plant Leaves for the Detection of Circular Leaf Spot Disease.

PubMed

Wijesinghe, Ruchire Eranga; Lee, Seung-Yeol; Kim, Pilun; Jung, Hee-Young; Jeon, Mansik; Kim, Jeehyun

2016-08-12

The feasibility of using the bio-photonic imaging technique to assess symptoms of circular leaf spot (CLS) disease in Diospyros kaki (persimmon) leaf samples was investigated. Leaf samples were selected from persimmon plantations and were categorized into three groups: healthy leaf samples, infected leaf samples, and healthy-looking leaf samples from infected trees. Visually non-identifiable reduction of the palisade parenchyma cell layer thickness is the main initial symptom, which occurs at the initial stage of the disease. Therefore, we established a non-destructive bio-photonic inspection method using a 1310 nm swept source optical coherence tomography (SS-OCT) system. These results confirm that this method is able to identify morphological differences between healthy leaves from infected trees and leaves from healthy and infected trees. In addition, this method has the potential to generate significant cost savings and good control of CLS disease in persimmon fields.

Optical Inspection and Morphological Analysis of Diospyros kaki Plant Leaves for the Detection of Circular Leaf Spot Disease

PubMed Central

Wijesinghe, Ruchire Eranga; Lee, Seung-Yeol; Kim, Pilun; Jung, Hee-Young; Jeon, Mansik; Kim, Jeehyun

2016-01-01

The feasibility of using the bio-photonic imaging technique to assess symptoms of circular leaf spot (CLS) disease in Diospyros kaki (persimmon) leaf samples was investigated. Leaf samples were selected from persimmon plantations and were categorized into three groups: healthy leaf samples, infected leaf samples, and healthy-looking leaf samples from infected trees. Visually non-identifiable reduction of the palisade parenchyma cell layer thickness is the main initial symptom, which occurs at the initial stage of the disease. Therefore, we established a non-destructive bio-photonic inspection method using a 1310 nm swept source optical coherence tomography (SS-OCT) system. These results confirm that this method is able to identify morphological differences between healthy leaves from infected trees and leaves from healthy and infected trees. In addition, this method has the potential to generate significant cost savings and good control of CLS disease in persimmon fields. PMID:27529250

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

PubMed

Zwickl, Derrick J; Stein, Joshua C; Wing, Rod A; Ware, Doreen; Sanderson, Michael J

2014-09-01

We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and tree inference, the alignment software PRANK was used, and detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Testing aggregation hypotheses among Neotropical trees and shrubs: results from a 50-ha plot over 20 years of sampling.

PubMed

Myster, Randall W; Malahy, Michael P

2012-09-01

Spatial patterns of tropical trees and shrubs are important to understanding their interaction and the resultant structure of tropical rainforests. To assess this issue, we took advantage of previously collected data, on Neotropical tree and shrub stem identified to species and mapped for spatial coordinates in a 50ha plot, with a frequency of every five years and over a 20 year period. These stems data were first placed into four groups, regardless of species, depending on their location in the vertical strata of the rainforest (shrubs, understory trees, mid-sized trees, tall trees) and then used to generate aggregation patterns for each sampling year. We found shrubs and understory trees clumped at small spatial scales of a few meters for several of the years sampled. Alternatively, mid-sized trees and tall trees did not clump, nor did they show uniform (regular) patterns, during any sampling period. In general (1) groups found higher in the canopy did not show aggregation on the ground and (2) the spatial patterns of all four groups showed similarity among different sampling years, thereby supporting a "shifting mosaic" view of plant communities over large areas. Spatial analysis, such as this one, are critical to understanding and predicting tree spaces, tree-tree replacements and the Neotropical forest patterns, such as biodiversity and those needed for sustainability efforts, they produce.

Architecture of the wood-wide web: Rhizopogon spp. genets link multiple Douglas-fir cohorts.

PubMed

Beiler, Kevin J; Durall, Daniel M; Simard, Suzanne W; Maxwell, Sheri A; Kretzer, Annette M

2010-01-01

*The role of mycorrhizal networks in forest dynamics is poorly understood because of the elusiveness of their spatial structure. We mapped the belowground distribution of the fungi Rhizopogon vesiculosus and Rhizopogon vinicolor and interior Douglas-fir trees (Pseudotsuga menziesii var. glauca) to determine the architecture of a mycorrhizal network in a multi-aged old-growth forest. *Rhizopogon spp. mycorrhizas were collected within a 30 x 30 m plot. Trees and fungal genets were identified using multi-locus microsatellite DNA analysis. Tree genotypes from mycorrhizas were matched to reference trees aboveground. Two trees were considered linked if they shared the same fungal genet(s). *The two Rhizopogon species each formed 13-14 genets, each colonizing up to 19 trees in the plot. Rhizopogon vesiculosus genets were larger, occurred at greater depths, and linked more trees than genets of R. vinicolor. Multiple tree cohorts were linked, with young saplings established within the mycorrhizal network of Douglas-fir veterans. A strong positive relationship was found between tree size and connectivity, resulting in a scale-free network architecture with small-world properties. *This mycorrhizal network architecture suggests an efficient and robust network, where large trees play a foundational role in facilitating conspecific regeneration and stabilizing the ecosystem.

Modeling and experimental characterization of electromigration in interconnect trees

NASA Astrophysics Data System (ADS)

Thompson, C. V.; Hau-Riege, S. P.; Andleigh, V. K.

1999-11-01

Most modeling and experimental characterization of interconnect reliability is focussed on simple straight lines terminating at pads or vias. However, laid-out integrated circuits often have interconnects with junctions and wide-to-narrow transitions. In carrying out circuit-level reliability assessments it is important to be able to assess the reliability of these more complex shapes, generally referred to as `trees.' An interconnect tree consists of continuously connected high-conductivity metal within one layer of metallization. Trees terminate at diffusion barriers at vias and contacts, and, in the general case, can have more than one terminating branch when they include junctions. We have extended the understanding of `immortality' demonstrated and analyzed for straight stud-to-stud lines, to trees of arbitrary complexity. This leads to a hierarchical approach for identifying immortal trees for specific circuit layouts and models for operation. To complete a circuit-level-reliability analysis, it is also necessary to estimate the lifetimes of the mortal trees. We have developed simulation tools that allow modeling of stress evolution and failure in arbitrarily complex trees. We are testing our models and simulations through comparisons with experiments on simple trees, such as lines broken into two segments with different currents in each segment. Models, simulations and early experimental results on the reliability of interconnect trees are shown to be consistent.

The Occurrence of the Cicada Cicadatra persica on Apple Trees, Malus domestica, in Erneh, Syria

PubMed Central

Dardar, Marah A.; Belal, Hamzeh M.R.; Basheer, Abedlnabi M.

2013-01-01

An infestation of Cicadatra persica KirKaldy (Hemiptera: Cicadidae) on apple trees, Malus domestica Borkhausen (Rosales: Rosaceae), was reported for the first time in the apple fruit orchards of Erneh, Syria. Nymphs, adults, exuvia, and exit holes in the soil were observed. The species was identified as C. persica based on morphological characters. Some biological observations and an acoustic analysis of the male's songs were also achieved. PMID:23909877

Extreme Drought Events Revealed in Amazon Tree Ring Records

NASA Astrophysics Data System (ADS)

Jenkins, H. S.; Baker, P. A.; Guilderson, T. P.

2010-12-01

The Amazon basin is a center of deep atmospheric convection and thus acts as a major engine for global hydrologic circulation. Yet despite its significance, a full understanding of Amazon rainfall variability remains elusive due to a poor historical record of climate. Temperate tree rings have been used extensively to reconstruct climate over the last thousand years, however less attention has been given to the application of dendrochronology in tropical regions, in large part due to a lower frequency of tree species known to produce annual rings. Here we present a tree ring record of drought extremes from the Madre de Dios region of southeastern Peru over the last 190 years. We confirm that tree ring growth in species Cedrela odorata is annual and show it to be well correlated with wet season precipitation. This correlation is used to identify extreme dry (and wet) events that have occurred in the past. We focus on drought events identified in the record as drought frequency is expected to increase over the Amazon in a warming climate. The Cedrela chronology records historic Amazon droughts of the 20th century previously identified in the literature and extends the record of drought for this region to the year 1816. Our analysis shows that there has been an increase in the frequency of extreme drought (mean recurrence interval = 5-6 years) since the turn of the 20th century and both Atlantic and Pacific sea surface temperature (SST) forcing mechanisms are implicated.

Creation and genomic analysis of irradiation hybrids in Populus

Treesearch

Matthew S. Zinkgraf; K. Haiby; M.C. Lieberman; L. Comai; I.M. Henry; Andrew Groover

2016-01-01

Establishing efficient functional genomic systems for creating and characterizing genetic variation in forest trees is challenging. Here we describe protocols for creating novel gene-dosage variation in Populus through gamma-irradiation of pollen, followed by genomic analysis to identify chromosomal regions that have been deleted or inserted in...

Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm.

PubMed

Seo, Joo-Hyun; Park, Jihyang; Kim, Eun-Mi; Kim, Juhan; Joo, Keehyoung; Lee, Jooyoung; Kim, Byung-Gee

2014-02-01

Sequence subgrouping for a given sequence set can enable various informative tasks such as the functional discrimination of sequence subsets and the functional inference of unknown sequences. Because an identity threshold for sequence subgrouping may vary according to the given sequence set, it is highly desirable to construct a robust subgrouping algorithm which automatically identifies an optimal identity threshold and generates subgroups for a given sequence set. To meet this end, an automatic sequence subgrouping method, named 'Subgrouping Automata' was constructed. Firstly, tree analysis module analyzes the structure of tree and calculates the all possible subgroups in each node. Sequence similarity analysis module calculates average sequence similarity for all subgroups in each node. Representative sequence generation module finds a representative sequence using profile analysis and self-scoring for each subgroup. For all nodes, average sequence similarities are calculated and 'Subgrouping Automata' searches a node showing statistically maximum sequence similarity increase using Student's t-value. A node showing the maximum t-value, which gives the most significant differences in average sequence similarity between two adjacent nodes, is determined as an optimum subgrouping node in the phylogenetic tree. Further analysis showed that the optimum subgrouping node from SA prevents under-subgrouping and over-subgrouping. Copyright © 2013. Published by Elsevier Ltd.

[Infrared Spectrum Analysis of Propolis and Tree Gum Collected from Different Areas].

PubMed

Luo, Huo-lin; Liu, Xing-xing; Gong, Shang-ji; Guo, Xia-li; Luo, Li-ping

2015-11-01

Propolis possesses functions of antibacterial, antiviral, anticancer, and liver protection, and is known as the "purple gold", however, the phenomenon which making and selling of counterfeit are growing in intensity. In order to establish a authenticity and quality of propolis evaluation model, in this paper, forty-one Chinese propolis, one proplis from United States and two tree gums were used for experimental materials. The infrared spectrum collection was performed by Fourier transform infrared spectrometer, and principal component analysis (PCA) was used for data analysis. The result showed that, the intrared spectrum of propolis and tree gum were significantly different. The propolis characteristic peak only appeared in 2500-3500 and 400-1800 cm⁻¹. All propolis had two frequency region of characteristic peaks, 2849.08-2848.53 and 2917.74- 2916.76 cm⁻¹, but tree gum did not have characteristic peak in this region. The characteristic peaks of gum were in 1150-1300 and 1550-1650 cm⁻¹. Differences in these aspects can be used to distinguish propolis and gum, and can be used to identify true and false propolis. We use Qinghai propolis as a standard sample, in 42 samples, the matching degree of other propolis is > 80%. In addition, the result of PCA shows that tree gum and the propolis from different climate zone, or with different colors could be distinguished well. This paper firstly performed analysis on different propolis and gum by infrared spectrum, and a new method, for authenticity and quality of propolis identification, could be developed.

Dynamics of market correlations: taxonomy and portfolio analysis.

PubMed

Onnela, J-P; Chakraborti, A; Kaski, K; Kertész, J; Kanto, A

2003-11-01

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the "asset tree" has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for "business as usual" and "crash" periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

Impact of different types of tree nut, peanut, and soy nut consumption on serum C-reactive protein (CRP): A systematic review and meta-analysis of randomized controlled clinical trials.

PubMed

Mazidi, Mohsen; Rezaie, Peyman; Ferns, Gordon A; Gao, Hong-Kai

2016-11-01

The effects of different types of tree nut, peanut, and soy nut consumption on serum C - reactive protein (CRP) are not well established. we aimed to undertake a systematic review and meta-analysis of prospective studies to determine the effect of nut consumption (tree nuts, peanuts, and soy nuts) on serum CRP. PubMed-Medline, Web of Science, Cochrane Database, and Google Scholar databases were searched (up until April 20 2016) to identify prospective studies evaluating the impact of tree nut, peanut, and soy nut consumption on serum CRP. Random effects models meta-analysis was used for quantitative data synthesis. Sensitivity analysis was conducted using the leave-one-out method. Heterogeneity was quantitatively assessed using the I index. Systematic review registration: CRD42016038044. From a total of 844 entries identified via searches, 20 studies were included in the final selection. The meta-analysis indicated a nonsignificant increase in serum CRP concentrations following nut consumption (weighted mean difference [WMD] 0.17 mg/L, (95% CI -0.67 to 0.33, I 52.1%). The WMDs for IL6 was -0.06(ng/dL), (95% CI -0.69 to 0.56, I 9.6%), -0.71(mg/dL), (95% CI -1.11 to -0.30, I 6.3%), for leptin, and -0.60(mg/dL), (95% CI -1.88 to 0.68, I 5.6%) for adiponectin, and -0.18(mg/dL), (95% CI -1.24 to 0.88, I 9.3%) for IL10 and -0.37 (pg/mL), (95% CI -0.90 to 0.16, I 7.9%) for TNF-α. These findings were robust in sensitivity analyses. This meta-analysis suggests that nut consumption significantly decrease leptin while have no significant effect on CRP, IL6, adiponectin, IL10, and TNF-α.

Data Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Powell, Danny H; Elwood Jr, Robert H

2011-01-01

Analysis of the material protection, control, and accountability (MPC&A) system is necessary to understand the limits and vulnerabilities of the system to internal threats. A self-appraisal helps the facility be prepared to respond to internal threats and reduce the risk of theft or diversion of nuclear material. The material control and accountability (MC&A) system effectiveness tool (MSET) fault tree was developed to depict the failure of the MPC&A system as a result of poor practices and random failures in the MC&A system. It can also be employed as a basis for assessing deliberate threats against a facility. MSET uses faultmore » tree analysis, which is a top-down approach to examining system failure. The analysis starts with identifying a potential undesirable event called a 'top event' and then determining the ways it can occur (e.g., 'Fail To Maintain Nuclear Materials Under The Purview Of The MC&A System'). The analysis proceeds by determining how the top event can be caused by individual or combined lower level faults or failures. These faults, which are the causes of the top event, are 'connected' through logic gates. The MSET model uses AND-gates and OR-gates and propagates the effect of event failure using Boolean algebra. To enable the fault tree analysis calculations, the basic events in the fault tree are populated with probability risk values derived by conversion of questionnaire data to numeric values. The basic events are treated as independent variables. This assumption affects the Boolean algebraic calculations used to calculate results. All the necessary calculations are built into the fault tree codes, but it is often useful to estimate the probabilities manually as a check on code functioning. The probability of failure of a given basic event is the probability that the basic event primary question fails to meet the performance metric for that question. The failure probability is related to how well the facility performs the task identified in that basic event over time (not just one performance or exercise). Fault tree calculations provide a failure probability for the top event in the fault tree. The basic fault tree calculations establish a baseline relative risk value for the system. This probability depicts relative risk, not absolute risk. Subsequent calculations are made to evaluate the change in relative risk that would occur if system performance is improved or degraded. During the development effort of MSET, the fault tree analysis program used was SAPHIRE. SAPHIRE is an acronym for 'Systems Analysis Programs for Hands-on Integrated Reliability Evaluations.' Version 1 of the SAPHIRE code was sponsored by the Nuclear Regulatory Commission in 1987 as an innovative way to draw, edit, and analyze graphical fault trees primarily for safe operation of nuclear power reactors. When the fault tree calculations are performed, the fault tree analysis program will produce several reports that can be used to analyze the MPC&A system. SAPHIRE produces reports showing risk importance factors for all basic events in the operational MC&A system. The risk importance information is used to examine the potential impacts when performance of certain basic events increases or decreases. The initial results produced by the SAPHIRE program are considered relative risk values. None of the results can be interpreted as absolute risk values since the basic event probability values represent estimates of risk associated with the performance of MPC&A tasks throughout the material balance area (MBA). The RRR for a basic event represents the decrease in total system risk that would result from improvement of that one event to a perfect performance level. Improvement of the basic event with the greatest RRR value produces a greater decrease in total system risk than improvement of any other basic event. Basic events with the greatest potential for system risk reduction are assigned performance improvement values, and new fault tree calculations show the improvement in total system risk. The operational impact or cost-effectiveness from implementing the performance improvements can then be evaluated. The improvements being evaluated can be system performance improvements, or they can be potential, or actual, upgrades to the system. The RIR for a basic event represents the increase in total system risk that would result from failure of that one event. Failure of the basic event with the greatest RIR value produces a greater increase in total system risk than failure of any other basic event. Basic events with the greatest potential for system risk increase are assigned failure performance values, and new fault tree calculations show the increase in total system risk. This evaluation shows the importance of preventing performance degradation of the basic events. SAPHIRE identifies combinations of basic events where concurrent failure of the events results in failure of the top event.« less

Use of GLM approach to assess the responses of tropical trees to urban air pollution in relation to leaf functional traits and tree characteristics.

PubMed

Mukherjee, Arideep; Agrawal, Madhoolika

2018-05-15

Responses of urban vegetation to air pollution stress in relation to their tolerance and sensitivity have been extensively studied, however, studies related to air pollution responses based on different leaf functional traits and tree characteristics are limited. In this paper, we have tried to assess combined and individual effects of major air pollutants PM 10 (particulate matter ≤ 10 µm), TSP (total suspended particulate matter), SO 2 (sulphur dioxide), NO 2 (nitrogen dioxide) and O 3 (ozone) on thirteen tropical tree species in relation to fifteen leaf functional traits and different tree characteristics. Stepwise linear regression a general linear modelling approach was used to quantify the pollution response of trees against air pollutants. The study was performed for six successive seasons for two years in three distinct urban areas (traffic, industrial and residential) of Varanasi city in India. At all the study sites, concentrations of air pollutants, specifically PM (particulate matter) and NO 2 were above the specified standards. Distinct variations were recorded in all the fifteen leaf functional traits with pollution load. Caesalpinia sappan was identified as most tolerant species followed by Psidium guajava, Dalbergia sissoo and Albizia lebbeck. Stepwise regression analysis identified maximum response of Eucalyptus citriodora and P. guajava to air pollutants explaining overall 59% and 58% variability's in leaf functional traits, respectively. Among leaf functional traits, maximum effect of air pollutants was observed on non-enzymatic antioxidants followed by photosynthetic pigments and leaf water status. Among the pollutants, PM was identified as the major stress factor followed by O 3 explaining 47% and 33% variability's in leaf functional traits. Tolerance and pollution response were regulated by different tree characteristics such as height, canopy size, leaf from, texture and nature of tree. Outcomes of this study will help in urban forest development by selection of specific pollutant tolerant tree species and leaf traits, which is suitable as air pollution mitigation measure. Copyright © 2018 Elsevier Inc. All rights reserved.

Quantitative and qualitative characteristics of cell wall components and prenyl lipids in the leaves of Tilia x euchlora trees growing under salt stress.

PubMed

Milewska-Hendel, Anna; Baczewska, Aneta H; Sala, Katarzyna; Dmuchowski, Wojciech; Brągoszewska, Paulina; Gozdowski, Dariusz; Jozwiak, Adam; Chojnacki, Tadeusz; Swiezewska, Ewa; Kurczynska, Ewa

2017-01-01

The study was focused on assessing the presence of arabinogalactan proteins (AGPs) and pectins within the cell walls as well as prenyl lipids, sodium and chlorine content in leaves of Tilia x euchlora trees. The leaves that were analyzed were collected from trees with and without signs of damage that were all growing in the same salt stress conditions. The reason for undertaking these investigations was the observations over many years that indicated that there are trees that present a healthy appearance and trees that have visible symptoms of decay in the same habitat. Leaf samples were collected from trees growing in the median strip between roadways that have been intensively salted during the winter season for many years. The sodium content was determined using atomic spectrophotometry, chloride using potentiometric titration and poly-isoprenoids using HPLC/UV. AGPs and pectins were determined using immunohistochemistry methods. The immunohistochemical analysis showed that rhamnogalacturonans I (RG-I) and homogalacturonans were differentially distributed in leaves from healthy trees in contrast to leaves from injured trees. In the case of AGPs, the most visible difference was the presence of the JIM16 epitope. Chemical analyses of sodium and chloride showed that in the leaves from injured trees, the level of these ions was higher than in the leaves from healthy trees. Based on chromatographic analysis, four poly-isoprenoid alcohols were identified in the leaves of T. x euchlora. The levels of these lipids were higher in the leaves from healthy trees. The results suggest that the differences that were detected in the apoplast and symplasm may be part of the defensive strategy of T. x euchlora trees to salt stress, which rely on changes in the chemical composition of the cell wall with respect to the pectic and AGP epitopes and an increased synthesis of prenyl lipids.

Quantitative and qualitative characteristics of cell wall components and prenyl lipids in the leaves of Tilia x euchlora trees growing under salt stress

PubMed Central

Milewska-Hendel, Anna; Baczewska, Aneta H.; Sala, Katarzyna; Dmuchowski, Wojciech; Brągoszewska, Paulina; Gozdowski, Dariusz; Jozwiak, Adam; Chojnacki, Tadeusz; Swiezewska, Ewa; Kurczynska, Ewa

2017-01-01

The study was focused on assessing the presence of arabinogalactan proteins (AGPs) and pectins within the cell walls as well as prenyl lipids, sodium and chlorine content in leaves of Tilia x euchlora trees. The leaves that were analyzed were collected from trees with and without signs of damage that were all growing in the same salt stress conditions. The reason for undertaking these investigations was the observations over many years that indicated that there are trees that present a healthy appearance and trees that have visible symptoms of decay in the same habitat. Leaf samples were collected from trees growing in the median strip between roadways that have been intensively salted during the winter season for many years. The sodium content was determined using atomic spectrophotometry, chloride using potentiometric titration and poly-isoprenoids using HPLC/UV. AGPs and pectins were determined using immunohistochemistry methods. The immunohistochemical analysis showed that rhamnogalacturonans I (RG-I) and homogalacturonans were differentially distributed in leaves from healthy trees in contrast to leaves from injured trees. In the case of AGPs, the most visible difference was the presence of the JIM16 epitope. Chemical analyses of sodium and chloride showed that in the leaves from injured trees, the level of these ions was higher than in the leaves from healthy trees. Based on chromatographic analysis, four poly-isoprenoid alcohols were identified in the leaves of T. x euchlora. The levels of these lipids were higher in the leaves from healthy trees. The results suggest that the differences that were detected in the apoplast and symplasm may be part of the defensive strategy of T. x euchlora trees to salt stress, which rely on changes in the chemical composition of the cell wall with respect to the pectic and AGP epitopes and an increased synthesis of prenyl lipids. PMID:28234963

Application of Genomic Technologies to the Breeding of Trees

PubMed Central

Badenes, Maria L.; Fernández i Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J.

2016-01-01

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species. PMID:27895664

Application of Genomic Technologies to the Breeding of Trees.

PubMed

Badenes, Maria L; Fernández I Martí, Angel; Ríos, Gabino; Rubio-Cabetas, María J

2016-01-01

The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.

Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

PubMed Central

Lopez, David; Ribeiro, Sébastien; Label, Philippe; Fumanal, Boris; Venisse, Jean-Stéphane; Kohler, Annegret; de Oliveira, Ricardo R.; Labutti, Kurt; Lipzen, Anna; Lail, Kathleen; Bauer, Diane; Ohm, Robin A.; Barry, Kerrie W.; Spatafora, Joseph; Grigoriev, Igor V.; Martin, Francis M.; Pujade-Renaud, Valérie

2018-01-01

Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulent C. cassiicola isolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico prediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species (Colletotrichum acutatum, Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca, and Botrosphaeria dothidea) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understanding C. cassiicola virulence and host specialization mechanisms. PMID:29551995

Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors.

PubMed

Lopez, David; Ribeiro, Sébastien; Label, Philippe; Fumanal, Boris; Venisse, Jean-Stéphane; Kohler, Annegret; de Oliveira, Ricardo R; Labutti, Kurt; Lipzen, Anna; Lail, Kathleen; Bauer, Diane; Ohm, Robin A; Barry, Kerrie W; Spatafora, Joseph; Grigoriev, Igor V; Martin, Francis M; Pujade-Renaud, Valérie

2018-01-01

Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulent C. cassiicola isolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico prediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species ( Colletotrichum acutatum, Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca , and Botrosphaeria dothidea ) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understanding C. cassiicola virulence and host specialization mechanisms.

[Analysis of dietary pattern and diabetes mellitus influencing factors identified by classification tree model in adults of Fujian].

PubMed

Yu, F L; Ye, Y; Yan, Y S

2017-05-10

Objective: To find out the dietary patterns and explore the relationship between environmental factors (especially dietary patterns) and diabetes mellitus in the adults of Fujian. Methods: Multi-stage sampling method were used to survey residents aged ≥18 years by questionnaire, physical examination and laboratory detection in 10 disease surveillance points in Fujian. Factor analysis was used to identify the dietary patterns, while logistic regression model was applied to analyze relationship between dietary patterns and diabetes mellitus, and classification tree model was adopted to identify the influencing factors for diabetes mellitus. Results: There were four dietary patterns in the population, including meat, plant, high-quality protein, and fried food and beverages patterns. The result of logistic analysis showed that plant pattern, which has higher factor loading of fresh fruit-vegetables and cereal-tubers, was a protective factor for non-diabetes mellitus. The risk of diabetes mellitus in the population at T2 and T3 levels of factor score were 0.727 (95 %CI: 0.561-0.943) times and 0.736 (95 %CI : 0.573-0.944) times higher, respectively, than those whose factor score was in lowest quartile. Thirteen influencing factors and eleven group at high-risk for diabetes mellitus were identified by classification tree model. The influencing factors were dyslipidemia, age, family history of diabetes, hypertension, physical activity, career, sex, sedentary time, abdominal adiposity, BMI, marital status, sleep time and high-quality protein pattern. Conclusion: There is a close association between dietary patterns and diabetes mellitus. It is necessary to promote healthy and reasonable diet, strengthen the monitoring and control of blood lipids, blood pressure and body weight, and have good lifestyle for the prevention and control of diabetes mellitus.

Blooming Trees: Substructures and Surrounding Groups of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Yu, Heng; Diaferio, Antonaldo; Serra, Ana Laura; Baldi, Marco

2018-06-01

We develop the Blooming Tree Algorithm, a new technique that uses spectroscopic redshift data alone to identify the substructures and the surrounding groups of galaxy clusters, along with their member galaxies. Based on the estimated binding energy of galaxy pairs, the algorithm builds a binary tree that hierarchically arranges all of the galaxies in the field of view. The algorithm searches for buds, corresponding to gravitational potential minima on the binary tree branches; for each bud, the algorithm combines the number of galaxies, their velocity dispersion, and their average pairwise distance into a parameter that discriminates between the buds that do not correspond to any substructure or group, and thus eventually die, and the buds that correspond to substructures and groups, and thus bloom into the identified structures. We test our new algorithm with a sample of 300 mock redshift surveys of clusters in different dynamical states; the clusters are extracted from a large cosmological N-body simulation of a ΛCDM model. We limit our analysis to substructures and surrounding groups identified in the simulation with mass larger than 1013 h ‑1 M ⊙. With mock redshift surveys with 200 galaxies within 6 h ‑1 Mpc from the cluster center, the technique recovers 80% of the real substructures and 60% of the surrounding groups; in 57% of the identified structures, at least 60% of the member galaxies of the substructures and groups belong to the same real structure. These results improve by roughly a factor of two the performance of the best substructure identification algorithm currently available, the σ plateau algorithm, and suggest that our Blooming Tree Algorithm can be an invaluable tool for detecting substructures of galaxy clusters and investigating their complex dynamics.

Identifying and Selecting Plants for the Landscape. Volume 23, Number 5.

ERIC Educational Resources Information Center

Rodekohr, Sherie; Harris, Clark Richard

This handbook on identifying and selecting landscape plants can be used as a reference in landscaping courses or on an individual basis. The first of two sections, Identifying Plants for the Landscape, contains the following tables: shade tree identification; flowering tree identification; evergreen tree identification; flowering shrub…

Single nucleotide polymorphism analysis reveals heterogeneity within a seedling tree population of a polyembryonic mango cultivar.

PubMed

Winterhagen, Patrick; Wünsche, Jens-Norbert

2016-05-01

Within a polyembryonic mango seedling tree population, the genetic background of individuals should be identical because vigorous plants for cultivation are expected to develop from nucellar embryos representing maternal clones. Due to the fact that the mango cultivar 'Hôi' is assigned to the polyembryonic ecotype, an intra-cultivar variability of ethylene receptor genes was unexpected. Ethylene receptors in plants are conserved, but the number of receptors or receptor isoforms is variable regarding different plant species. However, it is shown here that the ethylene receptor MiETR1 is present in various isoforms within the mango cultivar 'Hôi'. The investigation of single nucleotide polymorphisms revealed that different MiETR1 isoforms can not be discriminated simply by individual single nucleotide exchanges but by the specific arrangement of single nucleotide polymorphisms at certain positions in the exons of MiETR1. Furthermore, an MiETR1 isoform devoid of introns in the genomic sequence was identified. The investigation demonstrates some limitations of high resolution melting and ScreenClust analysis and points out the necessity of sequencing to identify individual isoforms and to determine the variability within the tree population.

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

PubMed

Gregg, W C Thomas; Ather, S Hussain; Hahn, Matthew W

2017-11-01

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids-autopolyploids and allopolyploids-differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker's yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

MANPRINT Methods Monograph: Aiding the Development of Manpower-Based System Evaluation

DTIC Science & Technology

1989-06-01

zone below tree level where threats are known to be (the actual number of threats may vary). Weather conditions are VFR. The helicopter pops up to...12.0 Replace 13.3 Bearing, connecting Inspect 6.2 Replace 6.2 0105 Camshaft Inspect 7.2 Replace 7.2 Cover, cylinder head Inspect .2 (valve cover...matrix to analyze the data and identify task clusters. . Outputs and Use of Cluster Analysis 1. Hierarchical cluster tree (taxonomy) of system tasks will

The structure of western warbler assemblages: Analysis of foraging behavior and habitat selection in Oregon

USGS Publications Warehouse

Morrison, Michael L.

1981-01-01

This study examines the foraging behavior and habitat selection of a MacGillivray's (Oporornis tolmiei)-Orange-crowned (Vermivora celata)-Wilson's (Wilsonia pusilla) warbler assemblage that occurred on early-growth clearcuts in western Oregon during breeding. Sites were divided into two groups based on the presence or absence of deciduous trees. Density estimates for each species were nearly identical between site classes except for Wilson's, whose density declined on nondeciduous tree sites. Analysis of vegetation parameters within the territories of the species identified deciduous tree cover as the variable of primary importance in the separation of warblers on each site, so that the assemblage could be arranged on a continuum of increasing deciduous tree cover. MacGillivray's and Wilson's extensively used shrub cover and deciduous tree cover, respectively; Orange-crowns were associated with both vegetation types. When the deciduous tree cover was reduced, Orange-crowns concentrated foraging activities in shrub cover and maintained nondisturbance densities. Indices of foraging-height diversity showed a marked decrease after the removal of deciduous trees. All species except MacGillivray's foraged lower in the vegatative substrate on the nondeciduous tree sites; MacGillivray's concentrated foraging activities in the low shrub cover on both sites. Indices of foraging overlap revealed a general pattern of decreased segregation by habitat after removal of deciduous trees. I suggest that the basic patterns of foraging behavior and habitat selection evidenced today in western North America were initially developed by ancestral warblers before their invasion of the west. Species successfully colonizing western habitats were probably preadapted to the conditions they encountered, with new habitats occupied without obvious evolutionary modifications.

Transcriptomic Analysis of Phenotypic Changes in Birch (Betula platyphylla) Autotetraploids

PubMed Central

Mu, Huai-Zhi; Liu, Zi-Jia; Lin, Lin; Li, Hui-Yu; Jiang, Jing; Liu, Gui-Feng

2012-01-01

Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA) and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees. PMID:23202935

First typology of cacao (Theobroma cacao L.) systems in Colombian Amazonia, based on tree species richness, canopy structure and light availability.

PubMed

Suárez Salazar, Juan Carlos; Ngo Bieng, Marie Ange; Melgarejo, Luz Marina; Di Rienzo, Julio A; Casanoves, Fernando

2018-01-01

We present a typology of cacao agroforest systems in Colombian Amazonia. These systems had yet to be described in the literature, especially their potential in terms of biodiversity conservation. The systems studied are located in a post-conflict area, and a deforestation front in Colombian Amazonia. Cacao cropping systems are of key importance in Colombia: cacao plays a prime role in post conflict resolution, as cacao is a legal crop to replace illegal crops; cacao agroforests are expected to be a sustainable practice, promoting forest-friendly land use. We worked in 50 x 2000 m2 agroforest plots, in Colombian Amazonia. A cluster analysis was used to build a typology based on 28 variables characterised in each plot, and related to diversity, composition, spatial structure and light availability for the cacao trees. We included variables related to light availability to evaluate the amount of transmitted radiation to the cacao trees in each type, and its suitability for cacao ecophysiological development. We identified 4 types of cacao agroforests based on differences concerning tree species diversity and the impact of canopy spatial structure on light availability for the cacao trees in the understorey. We found 127 tree species in the dataset, with some exclusive species in each type. We also found that 3 out of the 4 types identified displayed an erosion of tree species diversity. This reduction in shade tree species may have been linked to the desire to reduce shade, but we also found that all the types described were compatible with good ecophysiological development of the cacao trees. Cacao agroforest systems may actually be achieving biodiversity conservation goals in Colombian Amazonia. One challenging prospect will be to monitor and encourage the conservation of tree species diversity in cacao agroforest systems during the development of these cropping systems, as a form of forest-friendly management enhancing sustainable peace building in Colombia.

Clustering Genes of Common Evolutionary History

PubMed Central

Gori, Kevin; Suchan, Tomasz; Alvarez, Nadir; Goldman, Nick; Dessimoz, Christophe

2016-01-01

Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent—due to events such as incomplete lineage sorting or horizontal gene transfer—it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such “process-agnostic” approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward’s method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta. We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl). PMID:26893301

Characterization of fungal antagonistic bacilli isolated from aerial roots of banyan (Ficus benghalensis) using intact-cell MALDI-TOF mass spectrometry (ICMS).

PubMed

Pathak, K V; Keharia, H

2013-05-01

To characterize fungal antagonistic bacilli isolated from aerial roots of banyan tree and identify the metabolites responsible for their antifungal activity. Seven gram positive, endospore-forming, rod-shaped endophytic bacterial strains exhibiting a broad-spectrum antifungal activity were isolated from the surface-sterilized aerial roots of banyan tree. The isolates designated as K1, A2, A4 and A12 were identified as Bacillus subtilis, whereas isolates A11 and A13 were identified as Bacillus amyloliquefaciens using Biolog Microbial Identification System. The antifungal lipopeptides, surfactins, iturins and fengycins with masses varying in the range from m/z 900 to m/z 1550 could be detected using intact-cell MALDI-TOF mass spectrometry (ICMS). On the basis of mass spectral and carbon source utilization profile, all seven endophytes could be distinguished from each other. Furthermore, ICMS analysis revealed higher extent of heterogeneity among iturins and fengycins produced by B. subtilis K1, correlating well with its higher antifungal activity in comparison with other isolates. Seven fungal antagonistic bacilli were isolated from aerial roots of banyan tree, exhibiting broad spectrum of antifungal activity, among which B. subtilis K1 isolate was found to be most potent. The ICMS analysis revealed that all these isolates produced cyclic lipopeptides belonging to surfactin, iturin and fengycin families and exhibited varying degree of heterogeneity. The endophytes are considered as a potential source of novel bioactive metabolites, and this study describes the potent fungal antagonistic bacilli from aerial roots of banyan tree. The isolates described in this study have a prospective application as biocontrol agents. Also ICMS analysis described in this study for characterization of antifungal metabolites produced by banyan endophytic bacilli may be used as a high throughput tool for screening of microbes producing novel cyclic lipopeptides. © 2013 The Society for Applied Microbiology.

Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

NASA Astrophysics Data System (ADS)

Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

2013-04-01

Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry.

PubMed

Engwegen, Judith Y M N; Helgason, Helgi H; Cats, Annemieke; Harris, Nathan; Bonfrer, Johannes M G; Schellens, Jan H M; Beijnen, Jos H

2006-03-14

To detect the new serum biomarkers for colorectal cancer (CRC) by serum protein profiling with surface-enhanced laser desorption ionisation--time of flight mass spectrometry (SELDI-TOF MS). Two independent serum sample sets were analysed separately with the ProteinChip technology (set A: 40 CRC+49 healthy controls; set B: 37 CRC+31 healthy controls), using chips with a weak cation exchange moiety and buffer pH 5. Discriminative power of differentially expressed proteins was assessed with a classification tree algorithm. Sensitivities and specificities of the generated classification trees were obtained by blindly applying data from set A to the generated trees from set B and vice versa. CRC serum protein profiles were also compared with those from breast, ovarian, prostate, and non-small cell lung cancer. Mass-to-charge ratios (m/z) 3.1x10(3), 3.3x10(3), 4.5x10(3), 6.6x10(3) and 28x10(3) were used as classifiers in the best-performing classification trees. Tree sensitivities and specificities were between 65% and 90%. Most of these discriminative m/z values were also different in the other tumour types investigated. M/z 3.3x10(3), main classifier in most trees, was a doubly charged form of the 6.6x10(3)-Da protein. The latter was identified as apolipoprotein C-I. M/z 3.1x10(3) was identified as an N-terminal fragment of albumin, and m/z 28x10(3) as apolipoprotein A-I. SELDI-TOF MS followed by classification tree pattern analysis is a suitable technique for finding new serum markers for CRC. Biomarkers can be identified and reproducibly detected in independent sample sets with high sensitivities and specificities. Although not specific for CRC, these biomarkers have a potential role in disease and treatment monitoring.

Multifunctional imaging signature for V-KI-RAS2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations in colorectal cancer.

PubMed

Miles, Kenneth A; Ganeshan, Balaji; Rodriguez-Justo, Manuel; Goh, Vicky J; Ziauddin, Zia; Engledow, Alec; Meagher, Marie; Endozo, Raymondo; Taylor, Stuart A; Halligan, Stephen; Ell, Peter J; Groves, Ashley M

2014-03-01

This study explores the potential for multifunctional imaging to provide a signature for V-KI-RAS2 Kirsten rat sarcoma viral oncogene homolog (KRAS) gene mutations in colorectal cancer. This prospective study approved by the institutional review board comprised 33 patients undergoing PET/CT before surgery for proven primary colorectal cancer. Tumor tissue was examined histologically for presence of the KRAS mutations and for expression of hypoxia-inducible factor-1 (HIF-1) and minichromosome maintenance protein 2 (mcm2). The following imaging parameters were derived for each tumor: (18)F-FDG uptake ((18)F-FDG maximum standardized uptake value [SUVmax]), CT texture (expressed as mean of positive pixels [MPP]), and blood flow measured by dynamic contrast-enhanced CT. A recursive decision tree was developed in which the imaging investigations were applied sequentially to identify tumors with KRAS mutations. Monte Carlo analysis provided mean values and 95% confidence intervals for sensitivity, specificity, and accuracy. The final decision tree comprised 4 decision nodes and 5 terminal nodes, 2 of which identified KRAS mutants. The true-positive rate, false-positive rate, and accuracy (95% confidence intervals) of the decision tree were 82.4% (63.9%-93.9%), 0% (0%-10.4%), and 90.1% (79.2%-96.0%), respectively. KRAS mutants with high (18)F-FDG SUVmax and low MPP showed greater frequency of HIF-1 expression (P = 0.032). KRAS mutants with low (18)F-FDG SUV(max), high MPP, and high blood flow expressed mcm2 (P = 0.036). Multifunctional imaging with PET/CT and recursive decision-tree analysis to combine measurements of tumor (18)F-FDG uptake, CT texture, and perfusion has the potential to identify imaging signatures for colorectal cancers with KRAS mutations exhibiting hypoxic or proliferative phenotypes.

Suberin-derived aliphatic monomers as biomarkers for SOM affected by root litter contribution

NASA Astrophysics Data System (ADS)

Kogel-Knabner, I.; Spielvogel, S.-; Prietzel, J.-

2012-12-01

The patchy distribution of trees and ground vegetation may have major impact on SOC variability and stability at the small scale. Knowledge about correlations between the pattern of tree and ground vegetation, SOC stocks in different soil depths and the contribution of root- vs. shoot-derived carbon to different SOC fractions is scarce. We have tested analysis of hydrolysable aliphatic monomers derived from the biopolyesters cutin- and suberin to investigate whether their composition can be traced back after decay and transformation into soil organic matter (SOM) to study SOM source, degradation, and stand history. The main objective of this study was to elucidate the relative abundance of cutin and suberin in different particle size and density fractions of a Norway spruce and a European beech site with increasing distance to stems. Soil samples, root, bark and needle/leave samples were analyzed for their cutin and/or suberin signature. Previous to isolation of bound lipids, sequential solvent extraction was used to remove free lipids and other solvent extractable compounds. Cutin- and suberin-derived monomers were extracted from the samples using base hydrolysis. Before analysis by Gas Chromatography/Mass Spectrometry (GC/MS), extracts were derivatized to convert compounds to trimethylsilyl derivatives. Statistical analysis identified four variables which as combined factors discriminated significantly between cutin and suberin based on their structural units. We found a relative enrichment of cutin and suberin contents in the occluded fraction at both sites that decreased with increasing distance to the trees. We conclude from our results that (i) patchy above- and belowground carbon input caused by heterogeneous distribution of trees and ground vegetation has major impact on SOC variability and stability at the small scale, (ii) tree species is an important factor influencing SOC heterogeneity at the stand scale due to pronounced differences in above- and belowground carbon input among the tree species and that (iii) forest conversion may substantially alter SOC stocks and spatial distribution. Suberin biomarkers can thus be used as indicators for the presence of root influence on SOM composition and for identifying root-affected soil compartments.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes

PubMed Central

2014-01-01

Background Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Results Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Conclusions Gene expression profiling and trait-associated transcript analysis using an apple F1 population readily identified genes physically linked to powdery mildew disease resistance and woolly apple aphid resistance loci. This result was especially useful in apple, where extreme levels of heterozygosity make the development of reliable DNA markers quite difficult. The results suggest that this approach could prove effective in crops with complicated genetics, or for which few genomic information resources are available. PMID:24708064

Provisional tree and shrub seed zones for the Great Plains

Treesearch

Richard A. Cunningham

1975-01-01

Seed collection zones are subdivisions of land areas established to identify seed sources and to control the movement of seed and planting stock. Seed zones are needed for many species because of the genetic variation associated with their geographic distribution. Zone boundaries may be delineated from experimental data that identify genetic variation, or by analysis...

Acknowledging Different Needs: Developing a Taxonomy of Welfare Leavers.

ERIC Educational Resources Information Center

Julnes, George; Hayashi, Kentaro; Anderson, Steven

2001-01-01

Used cluster analysis of survey data for 506 respondents to create a taxonomy of welfare leavers in Illinois based on their self-reported well-being after leaving welfare. Used classification tree analysis to identify factors associated with different types of leavers. Findings highlight the existence of many marginally successful leavers who…

Impact of different types of tree nut, peanut, and soy nut consumption on serum C-reactive protein (CRP)

PubMed Central

Mazidi, Mohsen; Rezaie, Peyman; Ferns, Gordon A.; Gao, Hong-kai

2016-01-01

Abstract Background: The effects of different types of tree nut, peanut, and soy nut consumption on serum C - reactive protein (CRP) are not well established. we aimed to undertake a systematic review and meta-analysis of prospective studies to determine the effect of nut consumption (tree nuts, peanuts, and soy nuts) on serum CRP. Method: PubMed-Medline, Web of Science, Cochrane Database, and Google Scholar databases were searched (up until April 20 2016) to identify prospective studies evaluating the impact of tree nut, peanut, and soy nut consumption on serum CRP. Random effects models meta-analysis was used for quantitative data synthesis. Sensitivity analysis was conducted using the leave-one-out method. Heterogeneity was quantitatively assessed using the I2 index. Systematic review registration: CRD42016038044. Results: From a total of 844 entries identified via searches, 20 studies were included in the final selection. The meta-analysis indicated a nonsignificant increase in serum CRP concentrations following nut consumption (weighted mean difference [WMD] 0.17 mg/L, (95% CI –0.67 to 0.33, I2 52.1%). The WMDs for IL6 was –0.06(ng/dL), (95% CI –0.69 to 0.56, I2 9.6%), –0.71(mg/dL), (95% CI –1.11 to –0.30, I2 6.3%), for leptin, and -0.60(mg/dL), (95% CI –1.88 to 0.68, I2 5.6%) for adiponectin, and −0.18(mg/dL), (95% CI –1.24 to 0.88, I2 9.3%) for IL10 and –0.37 (pg/mL), (95% CI –0.90 to 0.16, I2 7.9%) for TNF-α. These findings were robust in sensitivity analyses. Conclusions: This meta-analysis suggests that nut consumption significantly decrease leptin while have no significant effect on CRP, IL6, adiponectin, IL10, and TNF-α. PMID:27858850

Lidar-derived estimate and uncertainty of carbon sink in successional phases of woody encroachment

NASA Astrophysics Data System (ADS)

Sankey, Temuulen; Shrestha, Rupesh; Sankey, Joel B.; Hardegree, Stuart; Strand, Eva

2013-07-01

encroachment is a globally occurring phenomenon that contributes to the global carbon sink. The magnitude of this contribution needs to be estimated at regional and local scales to address uncertainties present in the global- and continental-scale estimates, and guide regional policy and management in balancing restoration activities, including removal of woody plants, with greenhouse gas mitigation goals. The objective of this study was to estimate carbon stored in various successional phases of woody encroachment. Using lidar measurements of individual trees, we present high-resolution estimates of aboveground carbon storage in juniper woodlands. Segmentation analysis of lidar point cloud data identified a total of 60,628 juniper tree crowns across four watersheds. Tree heights, canopy cover, and density derived from lidar were strongly correlated with field measurements of 2613 juniper stems measured in 85 plots (30 × 30 m). Aboveground total biomass of individual trees was estimated using a regression model with lidar-derived height and crown area as predictors (Adj. R2 = 0.76, p < 0.001, RMSE = 0.58 kg). The predicted mean aboveground woody carbon storage for the study area was 677 g/m2. Uncertainty in carbon storage estimates was examined with a Monte Carlo approach that addressed major error sources. Ranges predicted with uncertainty analysis in the mean, individual tree, aboveground woody C, and associated standard deviation were 0.35 - 143.6 kg and 0.5 - 1.25 kg, respectively. Later successional phases of woody encroachment had, on average, twice the aboveground carbon relative to earlier phases. Woody encroachment might be more successfully managed and balanced with carbon storage goals by identifying priority areas in earlier phases of encroachment where intensive treatments are most effective.

Lidar-derived estimate and uncertainty of carbon sink in successional phases of woody encroachment

USGS Publications Warehouse

Sankey, Temuulen; Shrestha, Rupesh; Sankey, Joel B.; Hardgree, Stuart; Strand, Eva

2013-01-01

Woody encroachment is a globally occurring phenomenon that contributes to the global carbon sink. The magnitude of this contribution needs to be estimated at regional and local scales to address uncertainties present in the global- and continental-scale estimates, and guide regional policy and management in balancing restoration activities, including removal of woody plants, with greenhouse gas mitigation goals. The objective of this study was to estimate carbon stored in various successional phases of woody encroachment. Using lidar measurements of individual trees, we present high-resolution estimates of aboveground carbon storage in juniper woodlands. Segmentation analysis of lidar point cloud data identified a total of 60,628 juniper tree crowns across four watersheds. Tree heights, canopy cover, and density derived from lidar were strongly correlated with field measurements of 2613 juniper stems measured in 85 plots (30 × 30 m). Aboveground total biomass of individual trees was estimated using a regression model with lidar-derived height and crown area as predictors (Adj. R2 = 0.76, p 2. Uncertainty in carbon storage estimates was examined with a Monte Carlo approach that addressed major error sources. Ranges predicted with uncertainty analysis in the mean, individual tree, aboveground woody C, and associated standard deviation were 0.35 – 143.6 kg and 0.5 – 1.25 kg, respectively. Later successional phases of woody encroachment had, on average, twice the aboveground carbon relative to earlier phases. Woody encroachment might be more successfully managed and balanced with carbon storage goals by identifying priority areas in earlier phases of encroachment where intensive treatments are most effective.

Geospatial Technologies and i-Tree Echo Inventory for Predicting Climate Change on Urban Environment

NASA Astrophysics Data System (ADS)

Sriharan, S.; Robinson, L.; Ghariban, N.; Comar, M.; Pope, B.; Frey, G.

2015-12-01

Urban forests can be useful both in mitigating climate change and in helping cities adapt to higher temperatures and other impacts of climate change. Understanding and managing the impacts of climate change on the urban forest trees and natural communities will help us maintain their environmental, cultural, and economic benefits. Tree Inventory can provide important information on tree species, height, crown width, overall condition, health and maintenance needs. This presentation will demonstrate that a trees database system is necessary for developing a sustainable urban tree program. Virginia State University (VSU) campus benefits from large number and diversity of trees that are helping us by cleaning the air, retaining water, and providing shade on the buildings to reduce energy cost. The objectives of this study were to develop campus inventory of the trees, identify the tree species, map the locations of the trees with user-friendly tools such as i-Tree Eco and geospatial technologies by assessing the cost/benefit of employing student labor for training and ground validation of the results, and help campus landscape managers implement adaptive responses to climate change impacts. Data was collected on the location, species, and size of trees by using i-Tree urban forestry analysis software. This data was transferred to i-Tree inventory system for demonstrating types of trees, diameter of the trees, height of the trees, and vintage of the trees. The study site was mapped by collecting waypoints with GPS (Global Positioning System) at the trees and uploading these waypoints in ArcMap. The results of this study showed that: (i) students make good field crews, (ii) if more trees were placed in the proper area, the heating and cooling costs will reduce, and (iii) trees database system is necessary for planning, designing, planting, and maintenance, and removal of campus trees Research sponsored by the NIFA Grant, "Urban Forestry Management" (2012-38821-20153).

[The Application of the Fault Tree Analysis Method in Medical Equipment Maintenance].

PubMed

Liu, Hongbin

2015-11-01

In this paper, the traditional fault tree analysis method is presented, detailed instructions for its application characteristics in medical instrument maintenance is made. It is made significant changes when the traditional fault tree analysis method is introduced into the medical instrument maintenance: gave up the logic symbolic, logic analysis and calculation, gave up its complicated programs, and only keep its image and practical fault tree diagram, and the fault tree diagram there are also differences: the fault tree is no longer a logical tree but the thinking tree in troubleshooting, the definition of the fault tree's nodes is different, the composition of the fault tree's branches is also different.

Dynamics of market correlations: Taxonomy and portfolio analysis

NASA Astrophysics Data System (ADS)

Onnela, J.-P.; Chakraborti, A.; Kaski, K.; Kertész, J.; Kanto, A.

2003-11-01

The time dependence of the recently introduced minimum spanning tree description of correlations between stocks, called the “asset tree” has been studied in order to reflect the financial market taxonomy. The nodes of the tree are identified with stocks and the distance between them is a unique function of the corresponding element of the correlation matrix. By using the concept of a central vertex, chosen as the most strongly connected node of the tree, an important characteristic is defined by the mean occupation layer. During crashes, due to the strong global correlation in the market, the tree shrinks topologically, and this is shown by a low value of the mean occupation layer. The tree seems to have a scale-free structure where the scaling exponent of the degree distribution is different for “business as usual” and “crash” periods. The basic structure of the tree topology is very robust with respect to time. We also point out that the diversification aspect of portfolio optimization results in the fact that the assets of the classic Markowitz portfolio are always located on the outer leaves of the tree. Technical aspects such as the window size dependence of the investigated quantities are also discussed.

A survival tree method for the analysis of discrete event times in clinical and epidemiological studies.

PubMed

Schmid, Matthias; Küchenhoff, Helmut; Hoerauf, Achim; Tutz, Gerhard

2016-02-28

Survival trees are a popular alternative to parametric survival modeling when there are interactions between the predictor variables or when the aim is to stratify patients into prognostic subgroups. A limitation of classical survival tree methodology is that most algorithms for tree construction are designed for continuous outcome variables. Hence, classical methods might not be appropriate if failure time data are measured on a discrete time scale (as is often the case in longitudinal studies where data are collected, e.g., quarterly or yearly). To address this issue, we develop a method for discrete survival tree construction. The proposed technique is based on the result that the likelihood of a discrete survival model is equivalent to the likelihood of a regression model for binary outcome data. Hence, we modify tree construction methods for binary outcomes such that they result in optimized partitions for the estimation of discrete hazard functions. By applying the proposed method to data from a randomized trial in patients with filarial lymphedema, we demonstrate how discrete survival trees can be used to identify clinically relevant patient groups with similar survival behavior. Copyright © 2015 John Wiley & Sons, Ltd.

A stochastic multiple imputation algorithm for missing covariate data in tree-structured survival analysis.

PubMed

Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati

2010-12-20

Missing covariate data present a challenge to tree-structured methodology due to the fact that a single tree model, as opposed to an estimated parameter value, may be desired for use in a clinical setting. To address this problem, we suggest a multiple imputation algorithm that adds draws of stochastic error to a tree-based single imputation method presented by Conversano and Siciliano (Technical Report, University of Naples, 2003). Unlike previously proposed techniques for accommodating missing covariate data in tree-structured analyses, our methodology allows the modeling of complex and nonlinear covariate structures while still resulting in a single tree model. We perform a simulation study to evaluate our stochastic multiple imputation algorithm when covariate data are missing at random and compare it to other currently used methods. Our algorithm is advantageous for identifying the true underlying covariate structure when complex data and larger percentages of missing covariate observations are present. It is competitive with other current methods with respect to prediction accuracy. To illustrate our algorithm, we create a tree-structured survival model for predicting time to treatment response in older, depressed adults. Copyright © 2010 John Wiley & Sons, Ltd.

A Mid-Layer Model for Human Reliability Analysis: Understanding the Cognitive Causes of Human Failure Events

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stacey M. L. Hendrickson; April M. Whaley; Ronald L. Boring

The Office of Nuclear Regulatory Research (RES) is sponsoring work in response to a Staff Requirements Memorandum (SRM) directing an effort to establish a single human reliability analysis (HRA) method for the agency or guidance for the use of multiple methods. As part of this effort an attempt to develop a comprehensive HRA qualitative approach is being pursued. This paper presents a draft of the method’s middle layer, a part of the qualitative analysis phase that links failure mechanisms to performance shaping factors. Starting with a Crew Response Tree (CRT) that has identified human failure events, analysts identify potential failuremore » mechanisms using the mid-layer model. The mid-layer model presented in this paper traces the identification of the failure mechanisms using the Information-Diagnosis/Decision-Action (IDA) model and cognitive models from the psychological literature. Each failure mechanism is grouped according to a phase of IDA. Under each phase of IDA, the cognitive models help identify the relevant performance shaping factors for the failure mechanism. The use of IDA and cognitive models can be traced through fault trees, which provide a detailed complement to the CRT.« less

Identification and expression profiling of novel plant cell wall degrading enzymes from a destructive pest of palm trees, Rhynchophorus ferrugineus.

PubMed

Antony, B; Johny, J; Aldosari, S A; Abdelazim, M M

2017-08-01

Plant cell wall degrading enzymes (PCWDEs) from insects were recently identified as a multigene family of proteins that consist primarily of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) and play essential roles in the degradation of the cellulose/hemicellulose/pectin network in the invaded host plant. Here we applied transcriptomic and degenerate PCR approaches to identify the PCWDEs from a destructive pest of palm trees, Rhynchophorus ferrugineus, followed by a gut-specific and stage-specific differential expression analysis. We identified a total of 27 transcripts encoding GH family members and three transcripts of the CE family with cellulase, hemicellulase and pectinase activities. We also identified two GH9 candidates, which have not previously been reported from Curculionidae. The gut-specific quantitative expression analysis identified key cellulases, hemicellulases and pectinases from R. ferrugineus. The expression analysis revealed a pectin methylesterase, RferCE8u02, and a cellulase, GH45c34485, which showed the highest gut enriched expression. Comparison of PCWDE expression patterns revealed that cellulases and pectinases are significantly upregulated in the adult stages, and we observed specific high expression of the hemicellulase RferGH16c4170. Overall, our study revealed the potential of PCWDEs from R. ferrugineus, which may be useful in biotechnological applications and may represent new tools in R. ferrugineus pest management strategies. © 2017 The Royal Entomological Society.

[Research on identification of species of fruit trees by spectral analysis].

PubMed

Xing, Dong-Xing; Chang, Qing-Rui

2009-07-01

Using the spectral reflectance data (R2) of canopies, the present paper identifies seven species of fruit trees bearing fruit in the fruit mature period. Firstly, it compares the fruit tree species identification capability of six kinds of satellite sensors and four kinds of vegetation index through re-sampling the spectral data with six kinds of pre-defined filter function and the related data processing of calculating vegetation indexes. Then, it structures a BP neural network model for identifying seven species of fruit trees on the basis of choosing the best transformation of R(lambda) and optimizing the model parameters. The main conclusions are: (1) the order of the identification capability of the six kinds of satellite sensors from strong to weak is: MODIS, ASTER, ETM+, HRG, QUICKBIRD and IKONOS; (2) among the four kinds of vegetation indexes, the identification capability of RVI is the most powerful, the next is NDVI, while the identification capability of SAVI or DVI is relatively weak; (3) The identification capability of RVI and NDVI calculated with the reflectance of near-infrared and red channels of ETM+ or MODIS sensor is relatively powerful; (4) Among R(lambda) and its 22 kinds of transformation data, d1 [log(1/R(lambda))](derivative gap is set 9 nm) is the best transformation for structuring BP neural network model; (5) The paper structures a 3-layer BP neural network model for identifying seven species of fruit trees using the best transformation of R(lambda) which is d1 [log(1/R(lambda))](derivative gap is set 9 nm).

CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

PubMed Central

2011-01-01

Background The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices. Results Using CDAO as the semantic back-end, we developed a triple-store, named CDAO-Store. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, nexml, and NEXUS formats can be imported and their CDAO representations added to the triple-store. Conclusions CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at http://www.cs.nmsu.edu/~cdaostore. PMID:21496247

Tree species and size structure of old-growth Douglas-fir forests in central western Oregon, USA

USGS Publications Warehouse

Poage, Nathan; Tappeiner, J. C.

2005-01-01

We characterized the structure of 91 old-growth forests dominated by Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), using inventory data from recent (1985a??1991) old-growth timber sales in western Oregon. The data were complete counts (i.e., censuses) of all live trees >20 cm diameter at breast height (dbh, measured at 1.4 m above the ground) over a mean area of 17.1 ha at each site. Across all sites, Douglas-fir accounted for 79% of the total basal area (m2/ha) of all species. The average density of trees >100 cm dbh was 19 trees/ha and 90% of these trees were Douglas-fir. Species other than Douglas-fir constituted only about 20% of the total basal area at each old-growth site, on average, but largely accounted for the structural variation between sites. We used multivariate techniques such as cluster analysis, indicator species analysis, and ordination with non-metric multidimensional scaling (NMS) to identify and characterize six structural groups in terms of basal area in different speciesa??diameter classes. Almost 97% of the structural information was captured by the first (r2 = 0.841) and second (r2 = 0.128) NMS ordination axis. Geographic information systems (GIS) analysis and NMS indicated that the structural differences among groups of sites were associated with moisture, temperature, and elevation gradients within the study area. This type of analysis can be used to help define differences among old-growth forests and to set local structural goals for growing forests with old-growth characteristics.

CDAO-store: ontology-driven data integration for phylogenetic analysis.

PubMed

Chisham, Brandon; Wright, Ben; Le, Trung; Son, Tran Cao; Pontelli, Enrico

2011-04-15

The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices. Using CDAO as the semantic back-end, we developed a triple-store, named CDAO-Store. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, nexml, and NEXUS formats can be imported and their CDAO representations added to the triple-store. CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at http://www.cs.nmsu.edu/~cdaostore.

Applying decision tree for identification of a low risk population for type 2 diabetes. Tehran Lipid and Glucose Study.

PubMed

Ramezankhani, Azra; Pournik, Omid; Shahrabi, Jamal; Khalili, Davood; Azizi, Fereidoun; Hadaegh, Farzad

2014-09-01

The aim of this study was to create a prediction model using data mining approach to identify low risk individuals for incidence of type 2 diabetes, using the Tehran Lipid and Glucose Study (TLGS) database. For a 6647 population without diabetes, aged ≥20 years, followed for 12 years, a prediction model was developed using classification by the decision tree technique. Seven hundred and twenty-nine (11%) diabetes cases occurred during the follow-up. Predictor variables were selected from demographic characteristics, smoking status, medical and drug history and laboratory measures. We developed the predictive models by decision tree using 60 input variables and one output variable. The overall classification accuracy was 90.5%, with 31.1% sensitivity, 97.9% specificity; and for the subjects without diabetes, precision and f-measure were 92% and 0.95, respectively. The identified variables included fasting plasma glucose, body mass index, triglycerides, mean arterial blood pressure, family history of diabetes, educational level and job status. In conclusion, decision tree analysis, using routine demographic, clinical, anthropometric and laboratory measurements, created a simple tool to predict individuals at low risk for type 2 diabetes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Spatial statistical analysis of basal stem root disease under natural field epidemic of oil palm

NASA Astrophysics Data System (ADS)

Kamu, Assis; Phin, Chong Khim; Seman, Idris Abu; Wan, Hoong Hak; Mun, Ho Chong

2015-02-01

Oil palm or scientifically known as Elaeis guineensis Jacq. is the most important commodity crop in Malaysia and has greatly contributed to the economy growth of the country. As far as disease is concerned in the industry, Basal Stem Rot (BSR) caused by Ganoderma boninence remains the most important disease. BSR disease is the most widely studied with information available for oil palm disease in Malaysia. However, there is still limited study on the spatial as well as temporal pattern or distribution of the disease especially under natural field epidemic condition in oil palm plantation. The objective of this study is to spatially identify the pattern of BSR disease under natural field epidemic using two geospatial analytical techniques, which are quadrat analysis for the first order properties of partial pattern analysis and nearest-neighbor analysis (NNA) for the second order properties of partial pattern analysis. Two study sites were selected with different age of tree. Both sites are located in Tawau, Sabah and managed by the same company. The results showed that at least one of the point pattern analysis used which is NNA (i.e. the second order properties of partial pattern analysis) has confirmed the disease is complete spatial randomness. This suggests the spread of the disease is not from tree to tree and the age of palm does not play a significance role in determining the spatial pattern of the disease. From the spatial pattern of the disease, it would help in the disease management program and for the industry in the future. The statistical modelling is expected to help in identifying the right model to estimate the yield loss of oil palm due to BSR disease in the future.

Comparison of optical properties of chromophoric dissolved organic matter (CDOM) in alpine lakes above or below the tree line: insights into sources of CDOM.

PubMed

Su, Yaling; Chen, Feizhou; Liu, Zhengwen

2015-05-01

Here we investigated absorption and fluorescence properties of chromophoric dissolved organic matter (CDOM) in 15 alpine lakes located below or above the tree line to determine its source and composition. The results indicate that the concentrations of CDOM in below-tree-line lakes are significantly higher than in above-tree-line lakes, as evidenced from the absorption coefficients of a250 and a365. The intensities of the protein-like and humic-like fluorescence in below-tree-line lakes are higher than in above-tree-line lakes as well. Three fluorescent components were identified using parallel factor analysis (PARAFAC) modelling. Component 1 is probably associated with biological degradation of terrestrial humic component. The terrestrial humic-like component 2 is only found in below-tree-line lakes. The protein-like or phenolic component 3 is dominant in above-tree-line lakes, which is probably more derived from autochthonous origin. In this study, (1) higher a250/a365 and S275-295 values indicate smaller molecular weights of CDOM in above-tree-line lakes than in below-tree-line lakes, and smaller molecular weights at the surface than at 2.0 m depth; (2) SUVA254 and FI255 results provide evidence of lower percent aromaticity of CDOM in above-tree-line lakes; and (3) FI310 and FI370 suggest a strong allochthonous origin at the surface in below-tree-line lakes, and more contribution from autochthonous biological and aquatic bacterial origin in above-tree-line lakes.

Population structure of Aphis spiraecola (Hemiptera: Aphididae) on pear trees in China identified using microsatellites.

PubMed

Cao, Jinjun; Li, Jie; Niu, Jianqun; Liu, Xiaoxia; Zhang, Qingwen

2012-04-01

The spiraea aphid (Aphis spiraecola Patch) is a primary pest of fruit trees, particularly pear trees in China. Despite the economic importance of this pest, little is known about its genetic structure or its patterns of dispersal at local and regional scales; however, knowledge of these characteristics is important for establishing effective control strategies for this pest. The genetic variability of 431 individuals from 21 populations on pear trees in China was investigated using eight polymorphic microsatellite loci. The high polymorphism of these markers was evident from the expected heterozygosity value (He = 0.824) and the Polymorphism Information Content (PIC = 0.805), indicating that the spiraea aphid maintains a high level of genetic diversity. The analysis of molecular variance revealed a middle level of population differentiation (F(ST) = 0.1478) among A. spiraecola populations. This result is consistent with the results of the STRUCTURE analysis (K = 3), the unweighted pair-group method with arithmetic average tree and the Mantel test (r = 0.6392; P < 0.05). Our results indicate high levels of genetic exchange in the spiraea aphid, possibly facilitated by geography and climate. Our findings emphasize the importance of considering regional differences in studies of population structure, even when strong isolation-by-distance influences the genetic population structure of species.

Identification of genes differentially expressed during interaction of Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia"

PubMed Central

2011-01-01

Background "Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia". Results We carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin β 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase β. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection. Conclusion The present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with "Candidatus Phytoplasma aurantifolia". These results should help to elucidate the molecular basis of the infection process and to identify genes that could be targeted to increase plant resistance and inhibit the growth and reproduction of the pathogen. PMID:21194490

The effects of urban warming on herbivore abundance and street tree condition.

PubMed

Dale, Adam G; Frank, Steven D

2014-01-01

Trees are essential to urban habitats because they provide services that benefit the environment and improve human health. Unfortunately, urban trees often have more herbivorous insect pests than rural trees but the mechanisms and consequences of these infestations are not well documented. Here, we examine how temperature affects the abundance of a scale insect, Melanaspis tenebricosa (Comstock) (Hemiptera: Diaspididae), on one of the most commonly planted street trees in the eastern U.S. Next, we examine how both pest abundance and temperature are associated with water stress, growth, and condition of 26 urban street trees. Although trees in the warmest urban sites grew the most, they were more water stressed and in worse condition than trees in cooler sites. Our analyses indicate that visible declines in tree condition were best explained by scale-insect infestation rather than temperature. To test the broader relevance of these results, we extend our analysis to a database of more than 2700 Raleigh, US street trees. Plotting these trees on a Landsat thermal image of Raleigh, we found that warmer sites had over 70% more trees in poor condition than those in cooler sites. Our results support previous studies linking warmer urban habitats to greater pest abundance and extend this association to show its effect on street tree condition. Our results suggest that street tree condition and ecosystem services may decline as urban expansion and global warming exacerbate the urban heat island effect. Although our non-probability sampling method limits our scope of inference, our results present a gloomy outlook for urban forests and emphasize the need for management tools. Existing urban tree inventories and thermal maps could be used to identify species that would be most suitable for urban conditions.

Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

PubMed Central

Wang, Boyi; Tan, Hua-Wei; Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Matsumoto, Tracie; Zhang, Dapeng

2015-01-01

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification. PMID:26504559

Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

PubMed

Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

2016-09-16

The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

Locating hardware faults in a data communications network of a parallel computer

DOEpatents

Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

2010-01-12

Hardware faults location in a data communications network of a parallel computer. Such a parallel computer includes a plurality of compute nodes and a data communications network that couples the compute nodes for data communications and organizes the compute node as a tree. Locating hardware faults includes identifying a next compute node as a parent node and a root of a parent test tree, identifying for each child compute node of the parent node a child test tree having the child compute node as root, running a same test suite on the parent test tree and each child test tree, and identifying the parent compute node as having a defective link connected from the parent compute node to a child compute node if the test suite fails on the parent test tree and succeeds on all the child test trees.

Reliability Practice at NASA Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Pruessner, Paula S.; Li, Ming

2008-01-01

This paper describes in brief the Reliability and Maintainability (R&M) Programs performed directly by the reliability branch at Goddard Space Flight Center (GSFC). The mission assurance requirements flow down is explained. GSFC practices for PRA, reliability prediction/fault tree analysis/reliability block diagram, FMEA, part stress and derating analysis, worst case analysis, trend analysis, limit life items are presented. Lessons learned are summarized and recommendations on improvement are identified.

Section-Based Tree Species Identification Using Airborne LIDAR Point Cloud

NASA Astrophysics Data System (ADS)

Yao, C.; Zhang, X.; Liu, H.

2017-09-01

The application of LiDAR data in forestry initially focused on mapping forest community, particularly and primarily intended for largescale forest management and planning. Then with the smaller footprint and higher sampling density LiDAR data available, detecting individual tree overstory, estimating crowns parameters and identifying tree species are demonstrated practicable. This paper proposes a section-based protocol of tree species identification taking palm tree as an example. Section-based method is to detect objects through certain profile among different direction, basically along X-axis or Y-axis. And this method improve the utilization of spatial information to generate accurate results. Firstly, separate the tree points from manmade-object points by decision-tree-based rules, and create Crown Height Mode (CHM) by subtracting the Digital Terrain Model (DTM) from the digital surface model (DSM). Then calculate and extract key points to locate individual trees, thus estimate specific tree parameters related to species information, such as crown height, crown radius, and cross point etc. Finally, with parameters we are able to identify certain tree species. Comparing to species information measured on ground, the portion correctly identified trees on all plots could reach up to 90.65 %. The identification result in this research demonstrate the ability to distinguish palm tree using LiDAR point cloud. Furthermore, with more prior knowledge, section-based method enable the process to classify trees into different classes.

Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple.

PubMed

Guitton, B; Kelner, J J; Celton, J M; Sabau, X; Renou, J P; Chagné, D; Costes, E

2016-02-29

The transition from vegetative to floral state in shoot apical meristems (SAM) is a key event in plant development and is of crucial importance for reproductive success. In perennial plants, this event is recurrent during tree life and subject to both within-tree and between-years heterogeneity. In the present study, our goal was to identify candidate processes involved in the repression or induction of flowering in apical buds of adult apple trees. Genes differentially expressed (GDE) were examined between trees artificially set in either 'ON' or 'OFF' situation, and in which floral induction (FI) was shown to be inhibited or induced in most buds, respectively, using qRT-PCR and microarray analysis. From the period of FI through to flower differentiation, GDE belonged to four main biological processes (i) response to stimuli, including response to oxidative stress; (ii) cellular processes, (iii) cell wall biogenesis, and (iv) metabolic processes including carbohydrate biosynthesis and lipid metabolic process. Several key regulator genes, especially TEMPRANILLO (TEM), FLORAL TRANSITION AT MERISTEM (FTM1) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) were found differentially expressed. Moreover, homologs of SPL and Leucine-Rich Repeat proteins were present under QTL zones previously detected for biennial bearing. This data set suggests that apical buds of 'ON' and 'OFF' trees were in different physiological states, resulting from different metabolic, hormonal and redox status which are likely to contribute to FI control in adult apple trees. Investigations on carbohydrate and hormonal fluxes from sources to SAM and on cell detoxification process are expected to further contribute to the identification of the underlying physiological mechanisms of FI in adult apple trees.

Integrating ecosystem services analysis into scenario planning practice: accounting for street tree benefits with i-Tree valuation in Central Texas.

PubMed

Hilde, Thomas; Paterson, Robert

2014-12-15

Scenario planning continues to gain momentum in the United States as an effective process for building consensus on long-range community plans and creating regional visions for the future. However, efforts to integrate more sophisticated information into the analytical framework to help identify important ecosystem services have lagged in practice. This is problematic because understanding the tradeoffs of land consumption patterns on ecological integrity is central to mitigating the environmental degradation caused by land use change and new development. In this paper we describe how an ecosystem services valuation model, i-Tree, was integrated into a mainstream scenario planning software tool, Envision Tomorrow, to assess the benefits of public street trees for alternative future development scenarios. The tool is then applied to development scenarios from the City of Hutto, TX, a Central Texas Sustainable Places Project demonstration community. The integrated tool represents a methodological improvement for scenario planning practice, offers a way to incorporate ecosystem services analysis into mainstream planning processes, and serves as an example of how open source software tools can expand the range of issues available for community and regional planning consideration, even in cases where community resources are limited. The tool also offers room for future improvements; feasible options include canopy analysis of various future land use typologies, as well as a generalized street tree model for broader U.S. application. Copyright © 2014 Elsevier Ltd. All rights reserved.

Radiocarbon Dating of an Olive Tree Cross-Section: New Insights on Growth Patterns and Implications for Age Estimation of Olive Trees.

PubMed

Ehrlich, Yael; Regev, Lior; Kerem, Zohar; Boaretto, Elisabetta

2017-01-01

The age of living massive olive trees is often assumed to be between hundreds and even thousands of years. These estimations are usually based on the girth of the trunk and an extrapolation based on a theoretical annual growth rate. It is difficult to objectively verify these claims, as a monumental tree may not be cut down for analysis of its cross-section. In addition, the inner and oldest part of the trunk in olive trees usually rots, precluding the possibility of carting out radiocarbon analysis of material from the first years of life of the tree. In this work we present a cross-section of an olive tree, previously estimated to be hundreds of years old, which was cut down post-mortem in 2013. The cross-section was radiocarbon dated at numerous points following the natural growth pattern, which was made possible to observe by viewing the entire cross-section. Annual growth rate values were calculated and compared between different radii. The cross-section also revealed a nearly independent segment of growth, which would clearly offset any estimations based solely on girth calculations. Multiple piths were identified, indicating the beginning of branching within the trunk. Different radii were found to have comparable growth rates, resulting in similar estimates dating the piths to the 19th century. The estimated age of the piths represent a terminus ante quem for the age of the tree, as these are piths of separate branches. However, the tree is likely not many years older than the dated piths, and certainly not centuries older. The oldest radiocarbon-datable material in this cross-section was less than 200 years old, which is in agreement with most other radiocarbon dates of internal wood from living olive trees, rarely older than 300 years.

Ectomycorrhizal fungal communities on seedlings and conspecific trees of Pinus mugo grown on the coastal dunes of the Curonian Spit in Lithuania.

PubMed

Aučina, Algis; Rudawska, Maria; Leski, Tomasz; Ryliškis, Darius; Pietras, Marcin; Riepšas, Edvardas

2011-04-01

Ectomycorrhizal (ECM) communities of mature trees and regenerating seedlings of a non-native tree species Pinus mugo grown in a harsh environment of the coastal region of the Curonian Spit National Park in Lithuania were assessed. We established three study sites (S1, S2, and S3) that were separated from each other by 15 km. The ECM species richness was rather low in particular for mature, 100-year-old trees: 12 ectomycorrhizal taxa were identified by molecular analysis from 11 distinguished morphotypes. All 12 taxa were present on seedlings and on mature trees, with between 8-11 and 9-11 taxa present on seedlings and mature trees, respectively. Cenococcum geophilum dominated all ECM communities, but the relative abundance of C. geophilum mycorrhizas was nearly two times higher on seedlings than on mature trees. Mycorrhizal associations formed by Wilcoxina sp., Lactarius rufus, and Russula paludosa were also abundant. Several fungal taxa were only occasionally detected, including Cortinarius sp., Cortinarius obtusus, Cortinarius croceus, and Meliniomyces sp. Shannon's diversity indices for the ECM assemblages of P. mugo ranged from 0.98 to 1.09 for seedling and from 1.05 to 1.31 for mature trees. According to analysis of similarity, the mycorrhizal communities were similar between the sites (R = 0.085; P = 0.06) and only slightly separated between seedlings and mature trees (R = 0.24; P < 0.0001). An incidental fruiting body survey that was conducted weakly reflected the below-ground assessment of the ECM fungal community and once again showed that ECM and fruiting body studies commonly supply different partial accounts of the true ECM fungal diversity. Our results show that P. mugo has moved into quite distinct habitats and is able to adapt a suite of ECM symbionts that sufficiently support growth and development of this tree and allow for natural seedling regeneration.

A Voronoi interior adjacency-based approach for generating a contour tree

NASA Astrophysics Data System (ADS)

Chen, Jun; Qiao, Chaofei; Zhao, Renliang

2004-05-01

A contour tree is a good graphical tool for representing the spatial relations of contour lines and has found many applications in map generalization, map annotation, terrain analysis, etc. A new approach for generating contour trees by introducing a Voronoi-based interior adjacency set concept is proposed in this paper. The immediate interior adjacency set is employed to identify all of the children contours of each contour without contour elevations. It has advantages over existing methods such as the point-in-polygon method and the region growing-based method. This new approach can be used for spatial data mining and knowledge discovering, such as the automatic extraction of terrain features and construction of multi-resolution digital elevation model.

Microscopic saw mark analysis: an empirical approach.

PubMed

Love, Jennifer C; Derrick, Sharon M; Wiersema, Jason M; Peters, Charles

2015-01-01

Microscopic saw mark analysis is a well published and generally accepted qualitative analytical method. However, little research has focused on identifying and mitigating potential sources of error associated with the method. The presented study proposes the use of classification trees and random forest classifiers as an optimal, statistically sound approach to mitigate the potential for error of variability and outcome error in microscopic saw mark analysis. The statistical model was applied to 58 experimental saw marks created with four types of saws. The saw marks were made in fresh human femurs obtained through anatomical gift and were analyzed using a Keyence digital microscope. The statistical approach weighed the variables based on discriminatory value and produced decision trees with an associated outcome error rate of 8.62-17.82%. © 2014 American Academy of Forensic Sciences.

Application Research of Fault Tree Analysis in Grid Communication System Corrective Maintenance

NASA Astrophysics Data System (ADS)

Wang, Jian; Yang, Zhenwei; Kang, Mei

2018-01-01

This paper attempts to apply the fault tree analysis method to the corrective maintenance field of grid communication system. Through the establishment of the fault tree model of typical system and the engineering experience, the fault tree analysis theory is used to analyze the fault tree model, which contains the field of structural function, probability importance and so on. The results show that the fault tree analysis can realize fast positioning and well repairing of the system. Meanwhile, it finds that the analysis method of fault tree has some guiding significance to the reliability researching and upgrading f the system.

Identifying the performance characteristics of a winning outcome in elite mixed martial arts competition.

PubMed

James, Lachlan P; Robertson, Sam; Haff, G Gregory; Beckman, Emma M; Kelly, Vincent G

2017-03-01

To determine those performance indicators that have the greatest influence on classifying outcome at the elite level of mixed martial arts (MMA). A secondary objective was to establish the efficacy of decision tree analysis in explaining the characteristics of victory when compared to alternate statistical methods. Cross-sectional observational. Eleven raw performance indicators from male Ultimate Fighting Championship bouts (n=234) from July 2014 to December 2014 were screened for analysis. Each raw performance indicator was also converted to a rate-dependent measure to be scaled to fight duration. Further, three additional performance indicators were calculated from the dataset and included in the analysis. Cohen's d effect sizes were employed to determine the magnitude of the differences between Wins and Losses, while decision tree (chi-square automatic interaction detector (CHAID)) and discriminant function analyses (DFA) were used to classify outcome (Win and Loss). Effect size comparisons revealed differences between Wins and Losses across a number of performance indicators. Decision tree (raw: 71.8%; rate-scaled: 76.3%) and DFA (raw: 71.4%; rate-scaled 71.2%) achieved similar classification accuracies. Grappling and accuracy performance indicators were the most influential in explaining outcome. The decision tree models also revealed multiple combinations of performance indicators leading to victory. The decision tree analyses suggest that grappling activity and technique accuracy are of particular importance in achieving victory in elite-level MMA competition. The DFA results supported the importance of these performance indicators. Decision tree induction represents an intuitive and slightly more accurate approach to explaining bout outcome in this sport when compared to DFA. Copyright © 2016 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling.

PubMed

Dalmaris, Eleftheria; Ramalho, Cristina E; Poot, Pieter; Veneklaas, Erik J; Byrne, Margaret

2015-11-01

A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia. Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM). A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction. Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had contracted at the LGM. This signature of contraction from lower rainfall areas is consistent with current observations of decline on the semi-arid margin of the range, and indicates low capacity to tolerate forecast climatic change. Identification of a paleo-historical context for current tree decline enables conservation interventions to focus on maintaining genetic diversity, which provides the evolutionary potential for adaptation to climate change. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The risk factors of laryngeal pathology in Korean adults using a decision tree model.

PubMed

Byeon, Haewon

2015-01-01

The purpose of this study was to identify risk factors affecting laryngeal pathology in the Korean population and to evaluate the derived prediction model. Cross-sectional study. Data were drawn from the 2008 Korea National Health and Nutritional Examination Survey. The subjects were 3135 persons (1508 male and 2114 female) aged 19 years and older living in the community. The independent variables were age, sex, occupation, smoking, alcohol drinking, and self-reported voice problems. A decision tree analysis was done to identify risk factors for predicting a model of laryngeal pathology. The significant risk factors of laryngeal pathology were age, gender, occupation, smoking, and self-reported voice problem in decision tree model. Four significant paths were identified in the decision tree model for the prediction of laryngeal pathology. Those identified as high risk groups for laryngeal pathology included those who self-reported a voice problem, those who were males in their 50s who did not recognize a voice problem, those who were not economically active males in their 40s, and male workers aged 19 and over and under 50 or 60 and over who currently smoked. The results of this study suggest that individual risk factors, such as age, sex, occupation, health behavior, and self-reported voice problem, affect the onset of laryngeal pathology in a complex manner. Based on the results of this study, early management of the high-risk groups is needed for the prevention of laryngeal pathology. Copyright © 2015 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Determining Geometric Parameters of Agricultural Trees from Laser Scanning Data Obtained with Unmanned Aerial Vehicle

NASA Astrophysics Data System (ADS)

Hadas, E.; Jozkow, G.; Walicka, A.; Borkowski, A.

2018-05-01

The estimation of dendrometric parameters has become an important issue for agriculture planning and for the efficient management of orchards. Airborne Laser Scanning (ALS) data is widely used in forestry and many algorithms for automatic estimation of dendrometric parameters of individual forest trees were developed. Unfortunately, due to significant differences between forest and fruit trees, some contradictions exist against adopting the achievements of forestry science to agricultural studies indiscriminately. In this study we present the methodology to identify individual trees in apple orchard and estimate heights of individual trees, using high-density LiDAR data (3200 points/m2) obtained with Unmanned Aerial Vehicle (UAV) equipped with Velodyne HDL32-E sensor. The processing strategy combines the alpha-shape algorithm, principal component analysis (PCA) and detection of local minima. The alpha-shape algorithm is used to separate tree rows. In order to separate trees in a single row, we detect local minima on the canopy profile and slice polygons from alpha-shape results. We successfully separated 92 % of trees in the test area. 6 % of trees in orchard were not separated from each other and 2 % were sliced into two polygons. The RMSE of tree heights determined from the point clouds compared to field measurements was equal to 0.09 m, and the correlation coefficient was equal to 0.96. The results confirm the usefulness of LiDAR data from UAV platform in orchard inventory.

Analysis of occlusal variables, dental attrition, and age for distinguishing healthy controls from female patients with intracapsular temporomandibular disorders.

PubMed

Seligman, D A; Pullinger, A G

2000-01-01

Confusion about the relationship of occlusion to temporomandibular disorders (TMD) persists. This study attempted to identify occlusal and attrition factors plus age that would characterize asymptomatic normal female subjects. A total of 124 female patients with intracapsular TMD were compared with 47 asymptomatic female controls for associations to 9 occlusal factors, 3 attrition severity measures, and age using classification tree, multiple stepwise logistic regression, and univariate analyses. Models were tested for accuracy (sensitivity and specificity) and total contribution to the variance. The classification tree model had 4 terminal nodes that used only anterior attrition and age. "Normals" were mainly characterized by low attrition levels, whereas patients had higher attrition and tended to be younger. The tree model was only moderately useful (sensitivity 63%, specificity 94%) in predicting normals. The logistic regression model incorporated unilateral posterior crossbite and mediotrusive attrition severity in addition to the 2 factors in the tree, but was slightly less accurate than the tree (sensitivity 51%, specificity 90%). When only occlusal factors were considered in the analysis, normals were additionally characterized by a lack of anterior open bite, smaller overjet, and smaller RCP-ICP slides. The log likelihood accounted for was similar for both the tree (pseudo R(2) = 29.38%; mean deviance = 0.95) and the multiple logistic regression (Cox Snell R(2) = 30.3%, mean deviance = 0.84) models. The occlusal and attrition factors studied were only moderately useful in differentiating normals from TMD patients.

Risk assessment techniques with applicability in marine engineering

NASA Astrophysics Data System (ADS)

Rudenko, E.; Panaitescu, F. V.; Panaitescu, M.

2015-11-01

Nowadays risk management is a carefully planned process. The task of risk management is organically woven into the general problem of increasing the efficiency of business. Passive attitude to risk and awareness of its existence are replaced by active management techniques. Risk assessment is one of the most important stages of risk management, since for risk management it is necessary first to analyze and evaluate risk. There are many definitions of this notion but in general case risk assessment refers to the systematic process of identifying the factors and types of risk and their quantitative assessment, i.e. risk analysis methodology combines mutually complementary quantitative and qualitative approaches. Purpose of the work: In this paper we will consider as risk assessment technique Fault Tree analysis (FTA). The objectives are: understand purpose of FTA, understand and apply rules of Boolean algebra, analyse a simple system using FTA, FTA advantages and disadvantages. Research and methodology: The main purpose is to help identify potential causes of system failures before the failures actually occur. We can evaluate the probability of the Top event.The steps of this analize are: the system's examination from Top to Down, the use of symbols to represent events, the use of mathematical tools for critical areas, the use of Fault tree logic diagrams to identify the cause of the Top event. Results: In the finally of study it will be obtained: critical areas, Fault tree logical diagrams and the probability of the Top event. These results can be used for the risk assessment analyses.

Classification and ordination of understory vegetation using multivariate techniques in the Pinus wallichiana forests of Swat Valley, northern Pakistan

NASA Astrophysics Data System (ADS)

Rahman, Inayat Ur; Khan, Nasrullah; Ali, Kishwar

2017-04-01

An understory vegetation survey of the Pinus wallichiana-dominated temperate forests of Swat District was carried out to inspect the structure, composition and ecological associations of the forest vegetation. A quadrat method of sampling was used to record the floristic and phytosociological data necessary for the analysis using 300 quadrats of 10 × 10 m each. Some vegetation parameters viz. frequency and density for trees (overstory vegetation) as well as for the understory vegetation were recorded. The results revealed that in total, 92 species belonging to 77 different genera and 45 families existed in the area. The largest families were Asteraceae, Rosaceae and Lamiaceae with 12, ten and nine species, respectively. Ward's agglomerative cluster analysis for tree species resulted in three floristically and ecologically distinct community types along different topographic and soil variables. Importance value indices (IVI) were also calculated for understory vegetation and were subjected to ordination techniques, i.e. canonical correspondence analysis (CCA) and detrended correspondence analysis (DCA). DCA bi-plots for stands show that most of the stands were scattered around the centre of the DCA bi-plot, identified by two slightly scattered clusters. DCA for species bi-plot clearly identified three clusters of species revealing three types of understory communities in the study area. Results of the CCA were somewhat different from the DCA showing the impact of environmental variables on the understory species. CCA results reveal that three environmental variables, i.e. altitude, slope and P (mg/kg), have a strong influence on distribution of stands and species. Impact of tree species on the understory vegetation was also tested by CCA which showed that four tree species, i.e. P. wallichiana A.B. Jackson, Juglans regia Linn., Quercus dilatata Lindl. ex Royle and Cedrus deodara (Roxb. ex Lamb.) G. Don, have strong influences on associated understory vegetation. It is therefore concluded that Swat District has various microclimatic zones with suitable environmental variables to support distinct flora.

Identification of peanuts and tree nuts: are allergists smarter than their patients?

PubMed

Kao, Leon; Bhangoo, Parmbir S; Roy, Lonnie; Bird, J Andrew

2013-10-01

It has been reported that peanut- or tree nut-allergic individuals and their guardians are poorly capable of differentiating various tree nuts and peanuts. No information exists on the ability of allergists to differentiate peanuts and tree nuts. To measure the ability of allergists and other specialists within the allergy and immunology field to identify various types of tree nuts and peanuts. A nut box with a clear cover was constructed and contained various tree nuts and peanuts in shelled and unshelled forms. Attendees at the 2012 national meeting of the American Academy of Allergy, Asthma, and Immunology were offered participation by viewing the nut box and filling in their responses to a questionnaire. A similar procedure was conducted in the Food Allergy Center at Children's Medical Center (Dallas, TX) for guardians of children with and without peanut or tree nut allergies. Allergists were better able to identify and differentiate tree nuts and peanuts than guardians of peanut- or tree nut-allergic children, guardians of children without food allergies, and allergy and immunology fellows in training. It is important for allergists to educate peanut- and tree nut-allergic individuals and their guardians on the proper avoidance of peanuts and tree nuts. This includes education in the ability to identify peanuts and tree nuts. In addition, allergy and immunology fellows in training may benefit from education in proper peanut and tree nut identification. Copyright © 2013 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

How to Compare the Security Quality Requirements Engineering (SQUARE) Method with Other Methods

DTIC Science & Technology

2007-08-01

Attack Trees for Modeling and Analysis 10 2.8 Misuse and Abuse Cases 10 2.9 Formal Methods 11 2.9.1 Software Cost Reduction 12 2.9.2 Common...modern or efficient techniques. • Requirements analysis typically is either not performed at all (identified requirements are directly specified without...any analysis or modeling) or analysis is restricted to functional re- quirements and ignores quality requirements, other nonfunctional requirements

[Ecological indicators of habitat and biodiversity in a Neotropical landscape: multitaxonomic perspective].

PubMed

González-Valdivia, Noel; Ochoa-Gaona, Susana; Pozo, Carmen; Ferguson, Bruce Gordon; Rangel-Ruiz, Luis José; Arriaga-Weiss, Stefan Louis; Ponce-Mendoza, Alejandro; Kampichler, Christian

2011-09-01

Ecological indicators of habitat and biodiversity in a Neotropical landscape: multitaxonomic perspective. The use of indicator species to characterize specific ecological areas is of high importance in conservation/restoration biology. The objective of this study was to identify indicator species of diverse taxa that characterize different landscape units, and to better understand how management alters species composition. We identified two ecomosaics, tropical rain forest and the agricultural matrix, each one comprised of four landscape units. The taxonomic groups studied included birds (highly mobile), butterflies (moderately mobile), terrestrial gastropods (less mobile) and trees (sessile). Sampling efficiency for both ecomosaics was > or = 86%. We found 50 mollusks, 74 butterflies, 218 birds and 172 tree species, for a total of 514 species. Using ordination and cluster analysis, we distinguished three habitat types in the landscape: tropical rainforest, secondary vegetation and pastures with scattered trees and live fences. The InVal (> or = 50%) method identified 107 indicator species, including 45 tree species, 38 birds, 14 butterflies and 10 gastropods. Of these, 35 trees, 10 birds, four butterflies and eight gastropods were forest indicators. Additionally, 10, 28, 10 and two species, respectively per group, were characteristic of the agricultural matrix. Our results revealed a pattern of diversity decrease of indicator species along the rainforest-secondary forest-pasture gradient. In the forest, the gastropods Carychium exiguum, Coelocentrum turris, Glyphyalinia aff. indentata y Helicina oweniana were significantly correlated (p < 0.05) with 90% of the other groups of flora and fauna indicator species. These findings suggest that gastropods may be good indicators of forest habitat quality and biodiversity. The secondary vegetation is an intermediate disturbance phase that fosters high diversity in the agricultural matrix. We exemplify a multitaxa approach, including mesofauna, for ecological monitoring of agricultural landscapes.

First typology of cacao (Theobroma cacao L.) systems in Colombian Amazonia, based on tree species richness, canopy structure and light availability

PubMed Central

Suárez Salazar, Juan Carlos; Melgarejo, Luz Marina; Di Rienzo, Julio A.; Casanoves, Fernando

2018-01-01

Aim and background We present a typology of cacao agroforest systems in Colombian Amazonia. These systems had yet to be described in the literature, especially their potential in terms of biodiversity conservation. The systems studied are located in a post-conflict area, and a deforestation front in Colombian Amazonia. Cacao cropping systems are of key importance in Colombia: cacao plays a prime role in post conflict resolution, as cacao is a legal crop to replace illegal crops; cacao agroforests are expected to be a sustainable practice, promoting forest-friendly land use. Material and methods We worked in 50 x 2000 m2 agroforest plots, in Colombian Amazonia. A cluster analysis was used to build a typology based on 28 variables characterised in each plot, and related to diversity, composition, spatial structure and light availability for the cacao trees. We included variables related to light availability to evaluate the amount of transmitted radiation to the cacao trees in each type, and its suitability for cacao ecophysiological development. Main results We identified 4 types of cacao agroforests based on differences concerning tree species diversity and the impact of canopy spatial structure on light availability for the cacao trees in the understorey. We found 127 tree species in the dataset, with some exclusive species in each type. We also found that 3 out of the 4 types identified displayed an erosion of tree species diversity. This reduction in shade tree species may have been linked to the desire to reduce shade, but we also found that all the types described were compatible with good ecophysiological development of the cacao trees. Main conclusions and prospects Cacao agroforest systems may actually be achieving biodiversity conservation goals in Colombian Amazonia. One challenging prospect will be to monitor and encourage the conservation of tree species diversity in cacao agroforest systems during the development of these cropping systems, as a form of forest-friendly management enhancing sustainable peace building in Colombia. PMID:29401499

Dendrogeochronologic and Anatomic Analysis of Excavated Plains Cottonwoods Determine Overbank Sedimentation Rates and Historical Channel Positions Along the Interior of a Migrating Meander Bend, Powder River, Montana

NASA Astrophysics Data System (ADS)

Metzger, T. L.; Pizzuto, J. E.; Schook, D. M.; Hasse, T. R.; Affinito, R. A.

2017-12-01

Dendrochronological dating of buried trees precisely determines the germination year and identifies the stratigraphic context of germination for the trees. This recently developed application of dendrochronology provides accurate time-averaged sedimentation rates of overbank deposition along floodplains and can be used to identify burial events. Previous studies have demonstrated that tamarisk (Tamarix ramosissima) and sandbar willow (Salix exigua) develop anatomical changes within the tree rings (increased vessel size and decreased ring widths) on burial, but observations of plains cottonwood (Populus deltoides ssp. monilifera) are lacking. In September 2016 and June 2017, five buried plains cottonwoods were excavated along a single transect of the interior of a meander bend of the Powder River, Montana. Sediment samples were obtained near each tree for 210Pb and 137Cs dating, which will allow for comparison between dendrochronological and isotopic dating methods. The plains cottonwood samples collected exhibit anatomical changes associated with burial events that are observed in other species. All trees germinated at the boundary between thinly bedded fine sand and mud and coarse sand underlain by sand and gravel, indicating plains cottonwoods germinate on top of point bars prior to overbank deposition. The precise germination age and depth provide elevations and minimum age constraints for the point bar deposits and maximum ages for the overlying sediment, helping constrain past channel positions and overbank deposition rates. Germination years of the excavated trees, estimated from cores taken 1.5 m above ground level, range from 2014 to 1862. Accurate establishment years determined by cross-dating the buried section of the tree can add an additional 10 years to the cored age. The sedimentation rate and accumulation thickness varied with tree age. The germination year, total sediment accumulation, and average sedimentation rate at the five sampled trees is: 2011, 35 cm, 7.0 cm/year; 1973, 77 cm, 1.8 cm/year; 1962, 140 cm, 2.6 cm/year; 1960, 123 cm, 2.2 cm/year; and 1862, 112 cm, 0.7 cm/year. These sedimentation rates indicate that the cumulative sedimentation decreases as a power law with increasing tree age.

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences.

PubMed

Campbell, Matthew A; Alfaro, Michael E; Belasco, Max; López, J Andrés

2017-01-01

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides , monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.

Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

PubMed Central

Alfaro, Michael E.; Belasco, Max; López, J. Andrés

2017-01-01

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny. PMID:28929008

Is Susceptibility to Prenatal Methylmercury Exposure from Fish Consumption Non-Homogeneous? Tree-Structured Analysis for the Seychelles Child Development Study

PubMed Central

Huang, Li-Shan; Myers, Gary J.; Davidson, Philip W.; Cox, Christopher; Xiao, Fenyuan; Thurston, Sally W.; Cernichiari, Elsa; Shamlaye, Conrad F.; Sloane-Reeves, Jean; Georger, Lesley; Clarkson, Thomas W.

2007-01-01

Studies of the association between prenatal methylmercury exposure from maternal fish consumption during pregnancy and neurodevelopmental test scores in the Seychelles Child Development Study have found no consistent pattern of associations through age nine years. The analyses for the most recent nine-year data examined the population effects of prenatal exposure, but did not address the possibility of non-homogeneous susceptibility. This paper presents a regression tree approach: covariate effects are treated nonlinearly and non-additively and non-homogeneous effects of prenatal methylmercury exposure are permitted among the covariate clusters identified by the regression tree. The approach allows us to address whether children in the lower or higher ends of the developmental spectrum differ in susceptibility to subtle exposure effects. Of twenty-one endpoints available at age nine years, we chose the Weschler Full Scale IQ and its associated covariates to construct the regression tree. The prenatal mercury effect in each of the nine resulting clusters was assessed linearly and non-homogeneously. In addition we reanalyzed five other nine-year endpoints that in the linear analysis has a two-tailed p-value <0.2 for the effect of prenatal exposure. In this analysis, motor proficiency and activity level improved significantly with increasing MeHg for 53% of the children who had an average home environment. Motor proficiency significantly decreased with increasing prenatal MeHg exposure in 7% of the children whose home environment was below average. The regression tree results support previous analyses of outcomes in this cohort. However, this analysis raises the intriguing possibility that an effect may be non-homogeneous among children with different backgrounds and IQ levels. PMID:17942158

Is susceptibility to prenatal methylmercury exposure from fish consumption non-homogeneous? Tree-structured analysis for the Seychelles Child Development Study.

PubMed

Huang, Li-Shan; Myers, Gary J; Davidson, Philip W; Cox, Christopher; Xiao, Fenyuan; Thurston, Sally W; Cernichiari, Elsa; Shamlaye, Conrad F; Sloane-Reeves, Jean; Georger, Lesley; Clarkson, Thomas W

2007-11-01

Studies of the association between prenatal methylmercury exposure from maternal fish consumption during pregnancy and neurodevelopmental test scores in the Seychelles Child Development Study have found no consistent pattern of associations through age 9 years. The analyses for the most recent 9-year data examined the population effects of prenatal exposure, but did not address the possibility of non-homogeneous susceptibility. This paper presents a regression tree approach: covariate effects are treated non-linearly and non-additively and non-homogeneous effects of prenatal methylmercury exposure are permitted among the covariate clusters identified by the regression tree. The approach allows us to address whether children in the lower or higher ends of the developmental spectrum differ in susceptibility to subtle exposure effects. Of 21 endpoints available at age 9 years, we chose the Weschler Full Scale IQ and its associated covariates to construct the regression tree. The prenatal mercury effect in each of the nine resulting clusters was assessed linearly and non-homogeneously. In addition we reanalyzed five other 9-year endpoints that in the linear analysis had a two-tailed p-value <0.2 for the effect of prenatal exposure. In this analysis, motor proficiency and activity level improved significantly with increasing MeHg for 53% of the children who had an average home environment. Motor proficiency significantly decreased with increasing prenatal MeHg exposure in 7% of the children whose home environment was below average. The regression tree results support previous analyses of outcomes in this cohort. However, this analysis raises the intriguing possibility that an effect may be non-homogeneous among children with different backgrounds and IQ levels.

Testing the potential significance of different scion/rootstock genotype combinations on the ecology of old cultivated olive trees in the southeast Mediterranean area.

PubMed

Barazani, Oz; Waitz, Yoni; Tugendhaft, Yizhar; Dorman, Michael; Dag, Arnon; Hamidat, Mohammed; Hijawi, Thameen; Kerem, Zohar; Westberg, Erik; Kadereit, Joachim W

2017-02-06

A previous multi-locus lineage (MLL) analysis of SSR-microsatellite data of old olive trees in the southeast Mediterranean area had shown the predominance of the Souri cultivar (MLL1) among grafted trees. The MLL analysis had also identified an MLL (MLL7) that was more common among rootstocks than other MLLs. We here present a comparison of the MLL combinations MLL1 (scion)/MLL7 (rootstock) and MLL1/MLL1 in order to investigate the possible influence of rootstock on scion phenotype. A linear regression analysis demonstrated that the abundance of MLL1/MLL7 trees decreases and of MLL1/MLL1 trees increases along a gradient of increasing aridity. Hypothesizing that grafting on MLL7 provides an advantage under certain conditions, Akaike information criterion (AIC) model selection procedure was used to assess the influence of different environmental conditions on phenotypic characteristics of the fruits and oil of the two MLL combinations. The most parsimonious models indicated differential influences of environmental conditions on parameters of olive oil quality in trees belonging to the MLL1/MLL7 and MLL1/MLL1 combinations, but a similar influence on fruit characteristics and oil content. These results suggest that in certain environments grafting of the local Souri cultivar on MLL7 rootstocks and the MLL1/MLL1 combination result in improved oil quality. The decreasing number of MLL1/MLL7 trees along an aridity gradient suggests that use of this genotype combination in arid sites was not favoured because of sensitivity of MLL7 to drought. Our results thus suggest that MLL1/MLL7 and MLL1/MLL1 combinations were selected by growers in traditional rain-fed cultivation under Mediterranean climate conditions in the southeast Mediterranean area.

Moisture increase in response to high-altitude warming evidenced by tree-rings on the southeastern Tibetan Plateau

NASA Astrophysics Data System (ADS)

Li, Jinbao; Shi, Jiangfeng; Zhang, David D.; Yang, Bao; Fang, Keyan; Yue, Pak Hong

2017-01-01

Rapid warming has been observed in the high-altitude areas around the globe, but the implications on moisture change are not fully understood. Here we use tree-rings to reveal common moisture change on the southeastern Tibetan Plateau (TP) during the past five centuries, and show that regional moisture change in late spring to early summer (April-June) is closely related to large-scale temperature anomaly over the TP, with increased moisture coincident with periods of high temperature. The most recent pluvial during the 1990s-2000s is likely the wettest for the past five centuries, which coincides with the warmest period on the TP during the past millennium. Dynamic analysis reveals that vertical air convection is enhanced in response to anomalous TP surface warming, leading to an increase in lower-tropospheric humidity and effective precipitation over the southeastern TP. The coherent warm-wet relationship identified in both tree-rings and dynamic analysis implies a generally wetter condition on the southeastern TP under future warming.

Identification of subgroups by risk of graft failure after paediatric renal transplantation: application of survival tree models on the ESPN/ERA-EDTA Registry.

PubMed

Lofaro, Danilo; Jager, Kitty J; Abu-Hanna, Ameen; Groothoff, Jaap W; Arikoski, Pekka; Hoecker, Britta; Roussey-Kesler, Gwenaelle; Spasojević, Brankica; Verrina, Enrico; Schaefer, Franz; van Stralen, Karlijn J

2016-02-01

Identification of patient groups by risk of renal graft loss might be helpful for accurate patient counselling and clinical decision-making. Survival tree models are an alternative statistical approach to identify subgroups, offering cut-off points for covariates and an easy-to-interpret representation. Within the European Society of Pediatric Nephrology/European Renal Association-European Dialysis and Transplant Association (ESPN/ERA-EDTA) Registry data we identified paediatric patient groups with specific profiles for 5-year renal graft survival. Two analyses were performed, including (i) parameters known at time of transplantation and (ii) additional clinical measurements obtained early after transplantation. The identified subgroups were added as covariates in two survival models. The prognostic performance of the models was tested and compared with conventional Cox regression analyses. The first analysis included 5275 paediatric renal transplants. The best 5-year graft survival (90.4%) was found among patients who received a renal graft as a pre-emptive transplantation or after short-term dialysis (<45 days), whereas graft survival was poorest (51.7%) in adolescents transplanted after long-term dialysis (>2.2 years). The Cox model including both pre-transplant factors and tree subgroups had a significantly better predictive performance than conventional Cox regression (P < 0.001). In the analysis including clinical factors, graft survival ranged from 97.3% [younger patients with estimated glomerular filtration rate (eGFR) >30 mL/min/1.73 m(2) and dialysis <20 months] to 34.7% (adolescents with eGFR <60 mL/min/1.73 m(2) and dialysis >20 months). Also in this case combining tree findings and clinical factors improved the predictive performance as compared with conventional Cox model models (P < 0.0001). In conclusion, we demonstrated the tree model to be an accurate and attractive tool to predict graft failure for patients with specific characteristics. This may aid the evaluation of individual graft prognosis and thereby the design of measures to improve graft survival in the poor prognosis groups. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Assessment of Tree Leaves Flakes Mixed with Crude Glycerol as a Bioenergy Source

PubMed Central

Hilal-AlNaqbi, Ali; Al-Omari, Salah B.; Selim, Mohamed Y. E.

2016-01-01

The gasification and combustion of dry tree leaves and the cogasification of dry tree leaves soaking crude glycerol were studied experimentally. An updraft fixed bed gasification and combustion system was built. The operation was conducted at different air to fuel ratios. Results show more stable combustion and more effective heat transfer to furnace walls for the cases when tree leaves flakes are mixed with 20 percent (on mass basis) of crude glycerol, as compared with the case when only dry tree leaves are used as fuel. TGA analysis was also conducted for the two fuels used under both air and nitrogen environments. For the crude glycerol, four phases of pyrolysis and gasification were noticed under either of the two surrounding gaseous media (air or nitrogen). For the dry tree leaves, the pyrolysis under nitrogen shows only a simple smooth pyrolysis and gasification curve without showing the different distinct phases that were otherwise identified when the pyrolysis is conducted under air environment. Moreover, the air TGA results lead to more gasification due to the char oxidation at high temperatures. DTG results are also presented and discussed. PMID:27413749

Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness.

PubMed

Montoro, Pascal; Wu, Shuangyang; Favreau, Bénédicte; Herlinawati, Eva; Labrune, Cécile; Martin-Magniette, Marie-Laure; Pointet, Stéphanie; Rio, Maryannick; Leclercq, Julie; Ismawanto, Sigit; Kuswanhadi

2018-05-31

Tapping Panel Dryness (TPD) affects latex production in Hevea brasiliensis. This physiological syndrome involves the agglutination of rubber particles, which leads to partial or complete cessation of latex flow. Latex harvesting consists in tapping soft bark. Ethephon can be applied to stimulate latex flow and its regeneration in laticifers. Several studies have reported transcriptome changes in bark tissues. This study is the first report on deep RNA sequencing of latex to compare the effect of ethephon stimulation and TPD severity. Trees were carefully selected for paired-end sequencing using an Illumina HiSeq 2000. In all, 43 to 60 million reads were sequenced for each treatment in three biological replicates (slight TPD trees without ethephon stimulation, and slight and severe TPD trees with ethephon treatment). Differentially expressed genes were identified and annotated, giving 8,111 and 728 in response to ethephon in slight TPD trees and in ethephon-induced severe TPD trees, respectively. A biological network of responses to ethephon and TPD highlighted the major influence of metabolic processes and the response to stimulus, especially wounding and jasmonate depression in TPD-affected trees induced by ethephon stimulation.

Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

PubMed Central

Harris, Jordan Lee; Balci, Yilmaz

2015-01-01

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship. PMID:25815838

Variability in solar radiation and temperature explains observed patterns and trends in tree growth rates across four tropical forests.

PubMed

Dong, Shirley Xiaobi; Davies, Stuart J; Ashton, Peter S; Bunyavejchewin, Sarayudh; Supardi, M N Nur; Kassim, Abd Rahman; Tan, Sylvester; Moorcroft, Paul R

2012-10-07

The response of tropical forests to global climate variability and change remains poorly understood. Results from long-term studies of permanent forest plots have reported different, and in some cases opposing trends in tropical forest dynamics. In this study, we examined changes in tree growth rates at four long-term permanent tropical forest research plots in relation to variation in solar radiation, temperature and precipitation. Temporal variation in the stand-level growth rates measured at five-year intervals was found to be positively correlated with variation in incoming solar radiation and negatively related to temporal variation in night-time temperatures. Taken alone, neither solar radiation variability nor the effects of night-time temperatures can account for the observed temporal variation in tree growth rates across sites, but when considered together, these two climate variables account for most of the observed temporal variability in tree growth rates. Further analysis indicates that the stand-level response is primarily driven by the responses of smaller-sized trees (less than 20 cm in diameter). The combined temperature and radiation responses identified in this study provide a potential explanation for the conflicting patterns in tree growth rates found in previous studies.

Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

PubMed

Harris, Jordan Lee; Balci, Yilmaz

2015-01-01

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

Debris-flow activity in abandoned channels of the Manival torrent reconstructed with LiDAR and tree-ring data

NASA Astrophysics Data System (ADS)

Lopez Saez, J.; Corona, C.; Stoffel, M.; Gotteland, A.; Berger, F.; Liébault, F.

2011-05-01

Hydrogeomorphic processes are a major threat in many parts of the Alps, where they periodically damage infrastructure, disrupt transportation corridors or even cause loss of life. Nonetheless, past torrential activity and the analysis of areas affected during particular events remain often imprecise. It was therefore the purpose of this study to reconstruct spatio-temporal patterns of past debris-flow activity in abandoned channels on the forested cone of the Manival torrent (Massif de la Chartreuse, French Prealps). A Light Detecting and Ranging (LiDAR) generated Digital Elevation Model (DEM) was used to identify five abandoned channels and related depositional forms (lobes, lateral levees) in the proximal alluvial fan of the torrent. A total of 156 Scots pine trees (Pinus sylvestris L.) with clear signs of debris flow events was analyzed and growth disturbances (GD) assessed, such as callus tissue, the onset of compression wood or abrupt growth suppression. In total, 375 GD were identified in the tree-ring samples, pointing to 13 debris-flow events for the period 1931-2008. While debris flows appear to be very common at Manival, they have only rarely propagated outside the main channel over the past 80 years. Furthermore, analysis of the spatial distribution of disturbed trees contributed to the identification of four patterns of debris-flow routing and led to the determination of three preferential breakout locations. Finally, the results of this study demonstrate that the temporal distribution of debris flows did not exhibit significant variations since the beginning of the 20th century.

Taxonomic and ecological relevance of the chlorophyll a fluorescence signature of tree species in mixed European forests.

PubMed

Pollastrini, Martina; Holland, Vera; Brüggemann, Wolfgang; Bruelheide, Helge; Dănilă, Iulian; Jaroszewicz, Bogdan; Valladares, Fernando; Bussotti, Filippo

2016-10-01

The variability of chlorophyll a fluorescence (ChlF) parameters of forest tree species was investigated in 209 stands belonging to six European forests, from Mediterranean to boreal regions. The modifying role of environmental factors, forest structure and tree diversity (species richness and composition) on ChlF signature was analysed. At the European level, conifers showed higher potential performance than broadleaf species. Forests in central Europe performed better than those in Mediterranean and boreal regions. At the site level, homogeneous clusters of tree species were identified by means of a principal component analysis (PCA) of ChlF parameters. The discrimination of the clusters of species was influenced by their taxonomic position and ecological characteristics. The species richness influenced the tree ChlF properties in different ways depending on tree species and site. Tree species and site also affected the relationships between ChlF parameters and other plant functional traits (specific leaf area, leaf nitrogen content, light-saturated photosynthesis, wood density, leaf carbon isotope composition). The assessment of the photosynthetic properties of tree species, by means of ChlF parameters, in relation to their functional traits, is a relevant issue for studies in forest ecology. The connections of data from field surveys with remotely assessed parameters must be carefully explored. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Topographic influences on vegetation mosaics and tree diversity in the Chihuahuan Desert Borderlands.

PubMed

Poulos, Helen M; Camp, Ann E

2010-04-01

The abundance and distribution of species reflect how the niche requirements of species and the dynamics of populations interact with spatial and temporal variation in the environment. This study investigated the influence of geographical variation in environmental site conditions on tree dominance and diversity patterns in three topographically dissected mountain ranges in west Texas, USA, and northern Mexico. We measured tree abundance and basal area using a systematic sampling design across the forested areas of three mountain ranges and related these data to a suite of environmental parameters derived from field and digital elevation model data. We employed cluster analysis, classification and regression trees (CART), and rarefaction to identify (1) the dominant forest cover types across the three study sites and (2) environmental influences on tree distribution and diversity patterns. Elevation, topographic position, and incident solar radiation were the major influences on tree dominance and diversity. Mesic valley bottoms hosted high-diversity vegetation types, while hotter and drier mid-slopes and ridgetops supported lower tree diversity. Valley bottoms and other topographic positions shared few species, indicating high species turnover at the landscape scale. Mountain ranges with high topographic complexity also had higher species richness, suggesting that geographical variability in environmental conditions was a major influence on tree diversity. This study stressed the importance of landscape- and regional-scale topographic variability as a key factor controlling vegetation pattern and diversity in southwestern North America.

Acoustic analysis of warp potential of green ponderosa pine lumber

Treesearch

Xiping Wang; William T. Simpson

2005-01-01

This study evaluated the potential of acoustic analysis as presorting criteria to identify warp-prone boards before kiln drying. Dimension lumber, 38 by 89 mm (nominal 2 by 4 in.) and 2.44 m (8 ft) long, sawn from open-grown small-diameter ponderosa pine trees, was acoustically tested lengthwise at green condition. Three acoustic properties (acoustic speed, rate of...

Financial analysis of early stand treatments in southwest Oregon.

Treesearch

Helge Eng; K. Norman Johnson; Roger D. Fight

1990-01-01

Management guidelines for economically efficient early stand treatments were developed by identifying treatments that would maximize financial returns over the rotation for coast Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii) in southwest Oregon. Short rotations and low stand densities (trees per acre) gave...

Onboard Classifiers for Science Event Detection on a Remote Sensing Spacecraft

NASA Technical Reports Server (NTRS)

Castano, Rebecca; Mazzoni, Dominic; Tang, Nghia; Greeley, Ron; Doggett, Thomas; Cichy, Ben; Chien, Steve; Davies, Ashley

2006-01-01

Typically, data collected by a spacecraft is downlinked to Earth and pre-processed before any analysis is performed. We have developed classifiers that can be used onboard a spacecraft to identify high priority data for downlink to Earth, providing a method for maximizing the use of a potentially bandwidth limited downlink channel. Onboard analysis can also enable rapid reaction to dynamic events, such as flooding, volcanic eruptions or sea ice break-up. Four classifiers were developed to identify cryosphere events using hyperspectral images. These classifiers include a manually constructed classifier, a Support Vector Machine (SVM), a Decision Tree and a classifier derived by searching over combinations of thresholded band ratios. Each of the classifiers was designed to run in the computationally constrained operating environment of the spacecraft. A set of scenes was hand-labeled to provide training and testing data. Performance results on the test data indicate that the SVM and manual classifiers outperformed the Decision Tree and band-ratio classifiers with the SVM yielding slightly better classifications than the manual classifier.

Using fault tree analysis to identify contributing factors to engulfment in flowing grain in on-farm grain bins.

PubMed

Kingman, D M; Field, W E

2005-11-01

Findings reported by researchers at Illinois State University and Purdue University indicated that since 1980, an average of eight individuals per year have become engulfed and died in farm grain bins in the U.S. and Canada and that all these deaths are significant because they are believed to be preventable. During a recent effort to develop intervention strategies and recommendations for an ASAE farm grain bin safety standard, fault tree analysis (FTA) was utilized to identify contributing factors to engulfments in grain stored in on-farm grain bins. FTA diagrams provided a spatial perspective of the circumstances that occurred prior to engulfment incidents, a perspective never before presented in other hazard analyses. The FTA also demonstrated relationships and interrelationships of the contributing factors. FTA is a useful tool that should be applied more often in agricultural incident investigations to assist in the more complete understanding of the problem studied.

CircRNAs in the tree shrew (Tupaia belangeri) brain during postnatal development and aging.

PubMed

Lu, CaiXia; Sun, XiaoMei; Li, Na; Wang, WenGuang; Kuang, DeXuan; Tong, PinFen; Han, YuanYuan; Dai, JieJie

2018-04-30

Circular RNAs (circRNAs) are a novel type of non-coding RNA expressed across different species and tissues. At present, little is known about the expression and function of circRNAs in the tree shrew brain. In this study, we used RNA-seq to identify 35,007 circRNAs in hippocampus and cerebellum samples from infant (aged 47-52 days), young (aged 15-18 months), and old (aged 78-86 months) tree shrews. We observed no significant changes in the total circRNA expression profiles in different brain regions over time. However, circRNA tended to be downregulated in the cerebellum over time. Real-time RT-PCR analysis verified the presence of circRNAs. KEGG analysis indicated the occurrence of ubiquitin-mediated proteolysis, the MAPK signaling pathway, phosphatidylinositol signaling system, long-term depression, the rap1 signaling pathway, and long-term potentiation in both brain regions. We also observed that 29,087 (83.1%) tree shrew circRNAs shared homology with human circRNAs. The competing endogenous RNA networks suggested novel_circRNA_007362 potential functions as a 24-miRNAs sponge to regulate UBE4B expression. Thus, we obtained comprehensive circRNA expression profiles in the tree shrew brain during postnatal development and aging, which might help to elucidate the functions of circRNAs during brain aging and in age-related diseases.

Missing Rings in Pinus halepensis – The Missing Link to Relate the Tree-Ring Record to Extreme Climatic Events

PubMed Central

Novak, Klemen; de Luis, Martin; Saz, Miguel A.; Longares, Luis A.; Serrano-Notivoli, Roberto; Raventós, Josep; Čufar, Katarina; Gričar, Jožica; Di Filippo, Alfredo; Piovesan, Gianluca; Rathgeber, Cyrille B. K.; Papadopoulos, Andreas; Smith, Kevin T.

2016-01-01

Climate predictions for the Mediterranean Basin include increased temperatures, decreased precipitation, and increased frequency of extreme climatic events (ECE). These conditions are associated with decreased tree growth and increased vulnerability to pests and diseases. The anatomy of tree rings responds to these environmental conditions. Quantitatively, the width of a tree ring is largely determined by the rate and duration of cell division by the vascular cambium. In the Mediterranean climate, this division may occur throughout almost the entire year. Alternatively, cell division may cease during relatively cool and dry winters, only to resume in the same calendar year with milder temperatures and increased availability of water. Under particularly adverse conditions, no xylem may be produced in parts of the stem, resulting in a missing ring (MR). A dendrochronological network of Pinus halepensis was used to determine the relationship of MR to ECE. The network consisted of 113 sites, 1,509 trees, 2,593 cores, and 225,428 tree rings throughout the distribution range of the species. A total of 4,150 MR were identified. Binomial logistic regression analysis determined that MR frequency increased with increased cambial age. Spatial analysis indicated that the geographic areas of south-eastern Spain and northern Algeria contained the greatest frequency of MR. Dendroclimatic regression analysis indicated a non-linear relationship of MR to total monthly precipitation and mean temperature. MR are strongly associated with the combination of monthly mean temperature from previous October till current February and total precipitation from previous September till current May. They are likely to occur with total precipitation lower than 50 mm and temperatures higher than 5°C. This conclusion is global and can be applied to every site across the distribution area. Rather than simply being a complication for dendrochronology, MR formation is a fundamental response of trees to adverse environmental conditions. The demonstrated relationship of MR formation to ECE across this dendrochronological network in the Mediterranean basin shows the potential of MR analysis to reconstruct the history of past climatic extremes and to predict future forest dynamics in a changing climate. PMID:27303421

Missing Rings in Pinus halepensis - The Missing Link to Relate the Tree-Ring Record to Extreme Climatic Events.

PubMed

Novak, Klemen; de Luis, Martin; Saz, Miguel A; Longares, Luis A; Serrano-Notivoli, Roberto; Raventós, Josep; Čufar, Katarina; Gričar, Jožica; Di Filippo, Alfredo; Piovesan, Gianluca; Rathgeber, Cyrille B K; Papadopoulos, Andreas; Smith, Kevin T

2016-01-01

Climate predictions for the Mediterranean Basin include increased temperatures, decreased precipitation, and increased frequency of extreme climatic events (ECE). These conditions are associated with decreased tree growth and increased vulnerability to pests and diseases. The anatomy of tree rings responds to these environmental conditions. Quantitatively, the width of a tree ring is largely determined by the rate and duration of cell division by the vascular cambium. In the Mediterranean climate, this division may occur throughout almost the entire year. Alternatively, cell division may cease during relatively cool and dry winters, only to resume in the same calendar year with milder temperatures and increased availability of water. Under particularly adverse conditions, no xylem may be produced in parts of the stem, resulting in a missing ring (MR). A dendrochronological network of Pinus halepensis was used to determine the relationship of MR to ECE. The network consisted of 113 sites, 1,509 trees, 2,593 cores, and 225,428 tree rings throughout the distribution range of the species. A total of 4,150 MR were identified. Binomial logistic regression analysis determined that MR frequency increased with increased cambial age. Spatial analysis indicated that the geographic areas of south-eastern Spain and northern Algeria contained the greatest frequency of MR. Dendroclimatic regression analysis indicated a non-linear relationship of MR to total monthly precipitation and mean temperature. MR are strongly associated with the combination of monthly mean temperature from previous October till current February and total precipitation from previous September till current May. They are likely to occur with total precipitation lower than 50 mm and temperatures higher than 5°C. This conclusion is global and can be applied to every site across the distribution area. Rather than simply being a complication for dendrochronology, MR formation is a fundamental response of trees to adverse environmental conditions. The demonstrated relationship of MR formation to ECE across this dendrochronological network in the Mediterranean basin shows the potential of MR analysis to reconstruct the history of past climatic extremes and to predict future forest dynamics in a changing climate.

Dynamical mechanism in aero-engine gas path system using minimum spanning tree and detrended cross-correlation analysis

NASA Astrophysics Data System (ADS)

Dong, Keqiang; Zhang, Hong; Gao, You

2017-01-01

Identifying the mutual interaction in aero-engine gas path system is a crucial problem that facilitates the understanding of emerging structures in complex system. By employing the multiscale multifractal detrended cross-correlation analysis method to aero-engine gas path system, the cross-correlation characteristics between gas path system parameters are established. Further, we apply multiscale multifractal detrended cross-correlation distance matrix and minimum spanning tree to investigate the mutual interactions of gas path variables. The results can infer that the low-spool rotor speed (N1) and engine pressure ratio (EPR) are main gas path parameters. The application of proposed method contributes to promote our understanding of the internal mechanisms and structures of aero-engine dynamics.

A new fast method for inferring multiple consensus trees using k-medoids.

PubMed

Tahiri, Nadia; Willems, Matthieu; Makarenkov, Vladimir

2018-04-05

Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome. Many methods have been proposed to infer a single consensus tree from a collection of gene trees. Still, the application of these tree merging methods can lead to the loss of specific evolutionary patterns which characterize some gene families or some groups of gene families. Thus, the problem of inferring multiple consensus trees from a given set of gene trees becomes relevant. We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or taxa). The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees. We propose novel versions of the well-known Silhouette and Caliński-Harabasz cluster validity indices that are adapted for tree clustering with k-medoids. The efficiency of the new method was assessed using both synthetic and real data, such as a well-known phylogenetic dataset consisting of 47 gene trees inferred for 14 archaeal organisms. The method described here allows inference of multiple consensus trees from a given set of gene trees. It can be used to identify groups of gene trees having similar intragroup and different intergroup evolutionary histories. The main advantage of our method is that it is much faster than the existing tree clustering approaches, while providing similar or better clustering results in most cases. This makes it particularly well suited for the analysis of large genomic and phylogenetic datasets.

Demographic analysis of tree colonization in a 20-year-old right-of-way.

PubMed

Mercier, C; Brison, J; Bouchard, A

2001-12-01

Past tree colonization dynamics of a powerline-right-of-way (ROW) corridor in the Haut-Saint-Laurent region of Quebec was studied based on the present age distribution of its tree populations. This colonization study spans 20 years, from 1977 (ROW clearance) to 1996. The sampled quadrats were classified into six vegetation types. Tree colonization dynamics were interpreted in each type, and three distinct patterns were identified. (1) Communities adapted to acidic conditions were heavily colonized by Acer rubrum, at least for the last 12 years. (2) Communities adapted to mesic or to hydric conditions were more intensely colonized in the period 1985-1987 than in the following 9 years; this past success in tree colonization may have been caused by herbicide treatments, which could have facilitated tree establishment by damaging the herbaceous and shrub vegetation. (3) Cattail, vine-raspberry, and reed-dominated communities contained few tree individuals, with almost all trees establishing between 1979 and 1990; those three vegetation types appear as the most resistant to tree invasion in the ROW studied. This study supports the need for an integrated approach in ROW vegetation management, in which the selection of vegetation treatment methods would depend on the tree colonization dynamics in each vegetation type. Minimizing disturbances inflicted on ROW herbaceous and shrub covers should be the central strategy because disturbances jeopardize natural resistance to future tree invasion, except in communities adapted to acidic conditions where the existing vegetation does not prevent invasion by A. rubrum. Many trees are surviving the successive cutting operations by producing new sprouts each time, particularly in communities adapted to mesic and hydric conditions. In these cases, mechanical cutting should be replaced by a one-time stump-killing operation, to avoid repeated and unsuccessful treatments of the same individuals over time.

Topology of the correlation networks among major currencies using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Keskin, Mustafa; Deviren, Bayram; Kocakaplan, Yusuf

2011-02-01

We studied the topology of correlation networks among 34 major currencies using the concept of a minimal spanning tree and hierarchical tree for the full years of 2007-2008 when major economic turbulence occurred. We used the USD (US Dollar) and the TL (Turkish Lira) as numeraires in which the USD was the major currency and the TL was the minor currency. We derived a hierarchical organization and constructed minimal spanning trees (MSTs) and hierarchical trees (HTs) for the full years of 2007, 2008 and for the 2007-2008 period. We performed a technique to associate a value of reliability to the links of MSTs and HTs by using bootstrap replicas of data. We also used the average linkage cluster analysis for obtaining the hierarchical trees in the case of the TL as the numeraire. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial data. We illustrated how the minimal spanning trees and their related hierarchical trees developed over a period of time. From these trees we identified different clusters of currencies according to their proximity and economic ties. The clustered structure of the currencies and the key currency in each cluster were obtained and we found that the clusters matched nicely with the geographical regions of corresponding countries in the world such as Asia or Europe. As expected the key currencies were generally those showing major economic activity.

Integrated analysis of gene expression from carbon metabolism, proteome and metabolome, reveals altered primary metabolism in Eucalyptus grandis bark, in response to seasonal variation.

PubMed

Budzinski, Ilara Gabriela Frasson; Moon, David H; Morosini, Júlia Silva; Lindén, Pernilla; Bragatto, Juliano; Moritz, Thomaz; Labate, Carlos Alberto

2016-07-01

Seasonal variation is presumed to play an important role in the regulation of tree growth, especially for Eucalyptus grandis, a fast-growing tree. This variation may induce changes in the whole tree at transcriptional, protein and metabolite levels. Bark represents an important group of tissues that protect trees from desiccation and pathogen attack, and it has been identified as potential feedstock for lignocellulosic derived biofuels. Despite the growing interest, little is known about the molecular mechanisms that regulates bark metabolism, particularly in tropical countries. In this study we report the changes observed in the primary metabolism of E. grandis bark during two contrasting seasons in Brazil, summer (wet) and winter (dry), through the combination of transcripts (RT-qPCR), proteome (2-DE gels) and metabolome (GC-MS) analysis, in an integrated manner. Twenty-four genes, involved in carbon metabolism, were analyzed in the two seasons. Eleven were up-regulated in summer, three were up-regulated in winter and ten did not show statistical differences in the expression pattern. The proteomic analysis using 2-DE gels showed 77 proteins expressing differences in abundance, with 38 spots up-regulated in summer and 37 in winter. Different metabolites significantly accumulated during winter. This study revealed a metabolic reconfiguration in the primary metabolism of E. grandis bark, triggered by seasonal variation. Transcripts and protein data suggests that during winter carbohydrate formation seems to be favored by tree metabolism. Glucose, fructose and sucrose accumulated at significant levels during the winter.

A simple program to measure and analyse tree rings using Excel, R and SigmaScan

PubMed Central

Hietz, Peter

2011-01-01

I present a new software that links a program for image analysis (SigmaScan), one for spreadsheets (Excel) and one for statistical analysis (R) for applications of tree-ring analysis. The first macro measures ring width marked by the user on scanned images, stores raw and detrended data in Excel and calculates the distance to the pith and inter-series correlations. A second macro measures darkness along a defined path to identify latewood–earlywood transition in conifers, and a third shows the potential for automatic detection of boundaries. Written in Visual Basic for Applications, the code makes use of the advantages of existing programs and is consequently very economic and relatively simple to adjust to the requirements of specific projects or to expand making use of already available code. PMID:26109835

A simple program to measure and analyse tree rings using Excel, R and SigmaScan.

PubMed

Hietz, Peter

I present a new software that links a program for image analysis (SigmaScan), one for spreadsheets (Excel) and one for statistical analysis (R) for applications of tree-ring analysis. The first macro measures ring width marked by the user on scanned images, stores raw and detrended data in Excel and calculates the distance to the pith and inter-series correlations. A second macro measures darkness along a defined path to identify latewood-earlywood transition in conifers, and a third shows the potential for automatic detection of boundaries. Written in Visual Basic for Applications, the code makes use of the advantages of existing programs and is consequently very economic and relatively simple to adjust to the requirements of specific projects or to expand making use of already available code.

Applying fault tree analysis to the prevention of wrong-site surgery.

PubMed

Abecassis, Zachary A; McElroy, Lisa M; Patel, Ronak M; Khorzad, Rebeca; Carroll, Charles; Mehrotra, Sanjay

2015-01-01

Wrong-site surgery (WSS) is a rare event that occurs to hundreds of patients each year. Despite national implementation of the Universal Protocol over the past decade, development of effective interventions remains a challenge. We performed a systematic review of the literature reporting root causes of WSS and used the results to perform a fault tree analysis to assess the reliability of the system in preventing WSS and identifying high-priority targets for interventions aimed at reducing WSS. Process components where a single error could result in WSS were labeled with OR gates; process aspects reinforced by verification were labeled with AND gates. The overall redundancy of the system was evaluated based on prevalence of AND gates and OR gates. In total, 37 studies described risk factors for WSS. The fault tree contains 35 faults, most of which fall into five main categories. Despite the Universal Protocol mandating patient verification, surgical site signing, and a brief time-out, a large proportion of the process relies on human transcription and verification. Fault tree analysis provides a standardized perspective of errors or faults within the system of surgical scheduling and site confirmation. It can be adapted by institutions or specialties to lead to more targeted interventions to increase redundancy and reliability within the preoperative process. Copyright © 2015 Elsevier Inc. All rights reserved.

Identification of New Diterpenes as Putative Marker Compounds Distinguishing Agnus Castus Fruit (Chaste Tree) from Shrub Chaste Tree Fruit (Viticis Fructus).

PubMed

Oshima, Naohiro; Masada, Sayaka; Suzuki, Ryuta; Yagi, Kanae; Matsufuji, Hiroshi; Suenaga, Emi; Takahashi, Yutaka; Yahagi, Tadahiro; Watanabe, Masato; Yahara, Shoji; Iida, Osamu; Kawahara, Nobuo; Maruyama, Takuro; Goda, Yukihiro; Hakamatsuka, Takashi

2016-01-01

Agnus Castus Fruit is defined in the European Pharmacopoeia as the dried ripe fruit of Vitex agnus-castus. In Europe it is used as a medicine targeting premenstrual syndrome and climacteric disorder. In Japan, Agnus Castus Fruit is becoming popular as a raw material for over-the-counter drugs and health food products, though its congenic species, Vitex rotundifolia and Vitex trifolia, have been used as Shrub Chaste Tree Fruit in traditional medicines. Therefore, it is important to discriminate these Vitex plants from the viewpoint of regulatory science. Here we tried to identify putative marker compounds that distinguish between Agnus Castus Fruit and Shrub Chaste Tree Fruit. We analyzed extracts of each crude drug by liquid chromatography-mass spectrometry, and performed differential analysis by comparison of each chromatogram to find one or more peaks characteristic of Agnus Castus Fruit. A peak was isolated and identified as an equilibrium mixture of new compounds named chastol (1) and epichastol (1a). The planar structures of 1 and 1a were determined spectroscopically. Their relative configurations were revealed by nuclear Overhauser effect spectroscopy and differential nuclear Overhauser effect-NMR data. Since avoiding contamination from closely related species is needed for the quality control of natural pharmaceuticals, this information will be valuable to establish a method for the quality control of both, Agnus Castus Fruit and Shrub Chaste Tree Fruit products. Georg Thieme Verlag KG Stuttgart · New York.

Intra-urban biomonitoring: Source apportionment using tree barks to identify air pollution sources.

PubMed

Moreira, Tiana Carla Lopes; de Oliveira, Regiani Carvalho; Amato, Luís Fernando Lourenço; Kang, Choong-Min; Saldiva, Paulo Hilário Nascimento; Saiki, Mitiko

2016-05-01

It is of great interest to evaluate if there is a relationship between possible sources and trace elements using biomonitoring techniques. In this study, tree bark samples of 171 trees were collected using a biomonitoring technique in the inner city of São Paulo. The trace elements (Al, Ba, Ca, Cl, Cu, Fe, K, Mg, Mn, Na, P, Rb, S, Sr and Zn) were determined by the energy dispersive X-ray fluorescence (EDXRF) spectrometry. The Principal Component Analysis (PCA) was applied to identify the plausible sources associated with tree bark measurements. The greatest source was vehicle-induced non-tailpipe emissions derived mainly from brakes and tires wear-out and road dust resuspension (characterized with Al, Ba, Cu, Fe, Mn and Zn), which was explained by 27.1% of the variance, followed by cement (14.8%), sea salt (11.6%) and biomass burning (10%), and fossil fuel combustion (9.8%). We also verified that the elements related to vehicular emission showed different concentrations at different sites of the same street, which might be helpful for a new street classification according to the emission source. The spatial distribution maps of element concentrations were obtained to evaluate the different levels of pollution in streets and avenues. Results indicated that biomonitoring techniques using tree bark can be applied to evaluate dispersion of air pollution and provide reliable data for the further epidemiological studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tree Species Classification of Broadleaved Forests in Nagano, Central Japan, Using Airborne Laser Data and Multispectral Images

NASA Astrophysics Data System (ADS)

Deng, S.; Katoh, M.; Takenaka, Y.; Cheung, K.; Ishii, A.; Fujii, N.; Gao, T.

2017-10-01

This study attempted to classify three coniferous and ten broadleaved tree species by combining airborne laser scanning (ALS) data and multispectral images. The study area, located in Nagano, central Japan, is within the broadleaved forests of the Afan Woodland area. A total of 235 trees were surveyed in 2016, and we recorded the species, DBH, and tree height. The geographical position of each tree was collected using a Global Navigation Satellite System (GNSS) device. Tree crowns were manually detected using GNSS position data, field photographs, true-color orthoimages with three bands (red-green-blue, RGB), 3D point clouds, and a canopy height model derived from ALS data. Then a total of 69 features, including 27 image-based and 42 point-based features, were extracted from the RGB images and the ALS data to classify tree species. Finally, the detected tree crowns were classified into two classes for the first level (coniferous and broadleaved trees), four classes for the second level (Pinus densiflora, Larix kaempferi, Cryptomeria japonica, and broadleaved trees), and 13 classes for the third level (three coniferous and ten broadleaved species), using the 27 image-based features, 42 point-based features, all 69 features, and the best combination of features identified using a neighborhood component analysis algorithm, respectively. The overall classification accuracies reached 90 % at the first and second levels but less than 60 % at the third level. The classifications using the best combinations of features had higher accuracies than those using the image-based and point-based features and the combination of all of the 69 features.

Estimating urban trees and carbon stock potentials for mitigating climate change in Lagos: Case of Ikeja Government Reserved Area (GRA)

NASA Astrophysics Data System (ADS)

Elias, P. O.; Faderin, A.

2014-12-01

Urban trees are a component of the urban infrastructure which offers diverse services including environmental, aesthetic and economic. The accumulation of carbon in the atmosphere resulting from the indiscriminate distribution of human populations and urban activities with the unsustainable consumption of natural resources contributes to global environmental change especially in coastal cities like Lagos. Carbon stocks and sequestration by urban trees are increasingly recognized to play significant roles for mitigating climate change. This paper focuses on the estimation of carbon stock and sequestration through biomass estimation and quantification in Ikeja GRA, Lagos. Ikeja possesses a characteristic feature as a microcosm of Lagos due to the wide range of land uses. A canopy assessment of tree population was carried out using itree canopy software. A GPS survey was used to collect an inventory of all trees showing their location, spatial distribution and other attributes. The analysis of the carbon storage and sequestration potential of both actual and potential tree planting sites involved biomass estimations from tree allometry equations. Trees were identified at species level and measurements of their dendrometric values were recorded and integrated into the GIS database to estimate biomass of trees and carbon storage. The trees in the study area were estimated to have a biomass of 441.9 mg and carbon storage of 221.395 kg/tree. By considering the potential tree planting sites the estimated carbon stored increased to 11,352.73 kg. Carbon sequestration value in the study area was found to be 1.6790 tonnes for the existing trees and 40.707 tonnes for the potential tree planting sites (PTPS). The estimation of carbon storage and sequestration values of trees are important incentives for carbon accounting/footprints and monitoring of climate change mitigation which has implications for evaluation and monitoring of urban ecosystem.

Tree-space statistics and approximations for large-scale analysis of anatomical trees.

PubMed

Feragen, Aasa; Owen, Megan; Petersen, Jens; Wille, Mathilde M W; Thomsen, Laura H; Dirksen, Asger; de Bruijne, Marleen

2013-01-01

Statistical analysis of anatomical trees is hard to perform due to differences in the topological structure of the trees. In this paper we define statistical properties of leaf-labeled anatomical trees with geometric edge attributes by considering the anatomical trees as points in the geometric space of leaf-labeled trees. This tree-space is a geodesic metric space where any two trees are connected by a unique shortest path, which corresponds to a tree deformation. However, tree-space is not a manifold, and the usual strategy of performing statistical analysis in a tangent space and projecting onto tree-space is not available. Using tree-space and its shortest paths, a variety of statistical properties, such as mean, principal component, hypothesis testing and linear discriminant analysis can be defined. For some of these properties it is still an open problem how to compute them; others (like the mean) can be computed, but efficient alternatives are helpful in speeding up algorithms that use means iteratively, like hypothesis testing. In this paper, we take advantage of a very large dataset (N = 8016) to obtain computable approximations, under the assumption that the data trees parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than healthy ones. Software is available from http://image.diku.dk/aasa/software.php.

Ground water chlorinated ethenes in tree trunks: Case studies, influence of recharge, and potential degradation mechanism

USGS Publications Warehouse

Vroblesky, D.A.; Clinton, B.D.; Vose, J.M.; Casey, C.C.; Harvey, G.J.; Bradley, P.M.

2004-01-01

Trichloroethene (TCE) was detected in cores of trees growing above TCE-contaminated ground at three sites: the Carswell Golf Course in Texas, Air Force Plant PJKS in Colorado, and Naval Weapons Station Charleston in South Carolina. This was true even when the depth to water was 7.9 m or when the contaminated aquifer was confined beneath ???3 m of clay. Additional ground water contaminants detected in the tree cores were cis-1,2-dichloroethene at two sites and tetrachloroethene at one site. Thus, tree coring can be a rapid and effective means of locating shallow subsurface chlorinated ethenes and possibly identifying zones of active TCE dechlorination. Tree cores collected over time were useful in identifying the onset of ground water contamination. Several factors affecting chlorinated ethene concentrations in tree cores were identified in this investigation. The factors include ground water chlorinated ethene concentrations and depth to ground water contamination. In addition, differing TCE concentrations around the trunk of some trees appear to be related to the roots deriving water from differing areas. Opportunistic uptake of infiltrating rainfall can dilute prerain TCE concentrations in the trunk. TCE concentrations in core headspace may differ among some tree species. In some trees, infestation of bacteria in decaying heartwood may provide a TCE dechlorination mechanism within the trunk.

To core, or not to core: the impact of coring on tree health and a best-practice framework for collecting dendrochronological information from living trees.

PubMed

Tsen, Edward W J; Sitzia, Tommaso; Webber, Bruce L

2016-11-01

Trees are natural repositories of valuable environmental information that is preserved in the growth and structure of their stems, branches and roots. Dendrochronological analyses, based on the counting, crossdating and characterisation of incrementally formed wood rings, offer powerful insights for diverse fields including ecology, climatology and archaeology. The application of this toolset is likely to increase in popularity over coming decades due to advances in the field and a reduction in the cost of analyses. In research settings where the continued value of living trees subject to dendrochronological investigation is important, the use of an increment bore corer to extract trunk tissue is considered the best option to minimise negative impacts on tree health (e.g. stress and fitness). A small and fragmented body of literature, however, reports significant after-effects, and in some cases fatal outcomes, from this sampling technique. As it stands, the literature documenting increment bore coring (IBC) impacts lacks experimental consistency and is poorly replicated, making it difficult for prospective users of the method to assess likely tree responses to coring. This paucity of information has the potential to lead to destructive misuse of the method and also limits its safe implementation in circumstances where the risk of impacts may be appropriate. If IBC is to fulfil its potential as a method of choice across research fields, then we must first address our limited understanding of IBC impacts and provide a framework for its appropriate future use. Firstly, we review the historical context of studies examining the impacts of IBC on trees to identify known patterns, focal issues and biases in existing knowledge. IBC wound responses, particularly those that impact on lumber quality, have been the primary focus of prior studies. No universal treatment was identified that conclusively improved wound healing and few studies have linked wound responses to tree health impacts. Secondly, we build on literature insights using a theoretical approach to identify the most important factors to guide future research involving implementation of IBC, including innate tree characteristics and environmental factors. Thirdly, we synthesise and interrogate the quantitative data available through meta-analysis to identify risk factors for wound reactions. Although poor reporting standards, restricted scopes and a bias towards temperate ecosystems limited quantitative insight, we found that complete cambial wound closure could still harbour high rates of internal trunk decay, and that conditions favouring faster growth generally correlated with reduced indices of internal and external damage in broadleaved taxa. Finally, we propose a framework for guiding best-practice application of IBC to address knowledge gaps and maximise the utility of this method, including standardised reporting indices for identifying and minimising negative impacts on tree health. While IBC is an underutilised tool of ecological enquiry with broad applicability, the method will always incur some risk of negative impacts on the cored tree. We caution that the decision to core, or not to core, must be given careful consideration on a case-by-case basis. In time, we are confident that this choice will be better informed by evidence-based insight. © 2015 Cambridge Philosophical Society.

Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth.

PubMed

Wei, Hairong; Gou, Jiqing; Yordanov, Yordan; Zhang, Huaxin; Thakur, Ramesh; Jones, Wendy; Burton, Andrew

2013-03-01

Aspen (Populus tremuloides) trees growing under elevated [CO(2)] at a free-air CO(2) enrichment (FACE) site produced significantly more biomass than control trees. We investigated the molecular mechanisms underlying the observed increase in biomass by producing transcriptomic profiles of the vascular cambium zone (VCZ) and leaves, and then performed a comparative study to identify significantly changed genes and pathways after 12 years exposure to elevated [CO(2)]. In leaves, elevated [CO(2)] enhanced expression of genes related to Calvin cycle activity and linked pathways. In the VCZ, the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered while auxin conjugation, ABA synthesis, and cytokinin glucosylation and degradation were inhibited. Similarly, the genes involved in hemicellulose and pectin biosynthesis were enhanced, but some genes that catalyze important steps in lignin biosynthesis pathway were inhibited. Evidence from systemic analysis supported the functioning of multiple molecular mechanisms that underpin the enhanced radial growth in response to elevated [CO(2)].

Integrated Approach To Design And Analysis Of Systems

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Iverson, David L.

1993-01-01

Object-oriented fault-tree representation unifies evaluation of reliability and diagnosis of faults. Programming/fault tree described more fully in "Object-Oriented Algorithm For Evaluation Of Fault Trees" (ARC-12731). Augmented fault tree object contains more information than fault tree object used in quantitative analysis of reliability. Additional information needed to diagnose faults in system represented by fault tree.

Statistical indicators of collective behavior and functional clusters in gene networks of yeast

NASA Astrophysics Data System (ADS)

Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

2006-03-01

We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

Graph-associated entanglement cost of a multipartite state in exact and finite-block-length approximate constructions

NASA Astrophysics Data System (ADS)

Yamasaki, Hayata; Soeda, Akihito; Murao, Mio

2017-09-01

We introduce and analyze graph-associated entanglement cost, a generalization of the entanglement cost of quantum states to multipartite settings. We identify a necessary and sufficient condition for any multipartite entangled state to be constructible when quantum communication between the multiple parties is restricted to a quantum network represented by a tree. The condition for exact state construction is expressed in terms of the Schmidt ranks of the state defined with respect to edges of the tree. We also study approximate state construction and provide a second-order asymptotic analysis.

Application of ISO22000 and Failure Mode and Effect Analysis (fmea) for Industrial Processing of Poultry Products

NASA Astrophysics Data System (ADS)

Varzakas, Theodoros H.; Arvanitoyannis, Ioannis S.

Failure Mode and Effect Analysis (FMEA) model has been applied for the risk assessment of poultry slaughtering and manufacturing. In this work comparison of ISO22000 analysis with HACCP is carried out over poultry slaughtering, processing and packaging. Critical Control points and Prerequisite programs (PrPs) have been identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram and fishbone diagram).

Mixed-up trees: the structure of phylogenetic mixtures.

PubMed

Matsen, Frederick A; Mossel, Elchanan; Steel, Mike

2008-05-01

In this paper, we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster model, which is a generalization of the two state symmetric (CFN) model. In particular, we show that the set of mixture distributions forms a convex polytope and we calculate its dimension; corollaries include a simple criterion for when a mixture of branch lengths on the star tree can mimic the site pattern frequency vector of a resolved quartet tree. Furthermore, by computing volumes of polytopes we can clarify how "common" non-identifiable mixtures are under the CFN model. We also present a new combinatorial result which extends any identifiability result for a specific pair of trees of size six to arbitrary pairs of trees. Next we present a positive result showing identifiability of rates-across-sites models. Finally, we answer a question raised in a previous paper concerning "mixed branch repulsion" on trees larger than quartet trees under the CFN model.

Observations and Modelling of Alternative Tree Cover States of the Boreal Ecosystem

NASA Astrophysics Data System (ADS)

Abis, B.; Brovkin, V.

2017-12-01

Recently, multimodality of the tree cover distribution of the boreal forests has been detected, revealing the existence of three alternative vegetation modes. Identifying which are the regions with a potential for alternative tree cover states, and assessing which are the main factors underlying their existence, is important to project future change of natural vegetation cover and its effect on climate.Through the use of generalised additive models and phase-space analysis, we study the link between tree cover distribution and eight globally-observed environmental factors, such as rainfall, temperature, and permafrost distribution. Using a classification based on these factors, we show the location of areas with potentially alternative tree cover states under the same environmental conditions in the boreal region. Furthermore, to explain the multimodality found in the data and the asymmetry between North America and Eurasia, we study a conceptual model based on tree species competition, and use it to simulate the sensitivity of tree cover to changes in environmental factors.We find that the link between individual environmental variables and tree cover differs regionally. Nonetheless, environmental conditions uniquely determine the vegetation state among the three dominant modes in ˜95% of the cases. On the other hand, areas with potentially alternative tree cover states encompass ˜1.1 million km2, and correspond to possible transition zones with a reduced resilience to disturbances. Employing our conceptual model, we show that multimodality can be explained through competition between tree species with different adaptations to environmental factors and disturbances. Moreover, the model is able to reproduce the asymmetry in tree species distribution between Eurasia and North America. Finally, we find that changes in permafrost could be associated with bifurcation points of the model, corroborating the importance of permafrost in a changing climate.

An in situ approach to detect tree root ecology: linking ground-penetrating radar imaging to isotope-derived water acquisition zones

PubMed Central

Isaac, Marney E; Anglaaere, Luke C N

2013-01-01

Tree root distribution and activity are determinants of belowground competition. However, studying root response to environmental and management conditions remains logistically challenging. Methodologically, nondestructive in situ tree root ecology analysis has lagged. In this study, we tested a nondestructive approach to determine tree coarse root architecture and function of a perennial tree crop, Theobroma cacao L., at two edaphically contrasting sites (sandstone and phyllite–granite derived soils) in Ghana, West Africa. We detected coarse root vertical distribution using ground-penetrating radar and root activity via soil water acquisition using isotopic matching of δ18O plant and soil signatures. Coarse roots were detected to a depth of 50 cm, however, intraspecifc coarse root vertical distribution was modified by edaphic conditions. Soil δ18O isotopic signature declined with depth, providing conditions for plant–soil δ18O isotopic matching. This pattern held only under sandstone conditions where water acquisition zones were identifiably narrow in the 10–20 cm depth but broader under phyllite–granite conditions, presumably due to resource patchiness. Detected coarse root count by depth and measured fine root density were strongly correlated as were detected coarse root count and identified water acquisition zones, thus validating root detection capability of ground-penetrating radar, but exclusively on sandstone soils. This approach was able to characterize trends between intraspecific root architecture and edaphic-dependent resource availability, however, limited by site conditions. This study successfully demonstrates a new approach for in situ root studies that moves beyond invasive point sampling to nondestructive detection of root architecture and function. We discuss the transfer of such an approach to answer root ecology questions in various tree-based landscapes. PMID:23762519

Tapping the woodpecker tree for evolutionary insight.

PubMed

Shakya, Subir B; Fuchs, Jérôme; Pons, Jean-Marc; Sheldon, Frederick H

2017-11-01

Molecular phylogenetic studies of woodpeckers (Picidae) have generally focused on relationships within specific clades or have sampled sparsely across the family. We compared DNA sequences of six loci from 203 of the 217 recognized species of woodpeckers to construct a comprehensive tree of intrafamilial relationships. We recovered many known, but also numerous unknown, relationships among clades and species. We found, for example, that the three picine tribes are related as follows (Picini, (Campephilini, Melanerpini)) and that the genus Dinopium is paraphyletic. We used the tree to analyze rates of diversification and biogeographic patterns within the family. Diversification rate increased on two occasions during woodpecker history. We also tested diversification rates between temperate and tropical species but found no significant difference. Biogeographic analysis supported an Old World origin of the family and identified at least six independent cases of New World-Old World sister relationships. In light of the tree, we discuss how convergence, mimicry, and potential cases of hybridization have complicated woodpecker taxonomy. Copyright © 2017 Elsevier Inc. All rights reserved.

TreSpEx—Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

PubMed Central

Struck, Torsten H

2014-01-01

Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. The program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available at http://www.annelida.de/research/bioinformatics/software.html. PMID:24701118

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

PubMed Central

Nasr Esfahani, Bahram; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Moghoofei, Mohsen; Sedighi, Mansour; Hadifar, Shima

2016-01-01

Background Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study. Conclusions The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity. PMID:27284397

Automatic identification of origins of left and right coronary arteries in CT angiography for coronary arterial tree tracking and plaque detection

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Chan, Heang-Ping; Chightai, Aamer; Wei, Jun; Hadjiiski, Lubomir M.; Agarwal, Prachi; Kuriakose, Jean W.; Kazerooni, Ella A.

2013-03-01

Automatic tracking and segmentation of the coronary arterial tree is the basic step for computer-aided analysis of coronary disease. The goal of this study is to develop an automated method to identify the origins of the left coronary artery (LCA) and right coronary artery (RCA) as the seed points for the tracking of the coronary arterial trees. The heart region and the contrast-filled structures in the heart region are first extracted using morphological operations and EM estimation. To identify the ascending aorta, we developed a new multiscale aorta search method (MAS) method in which the aorta is identified based on a-priori knowledge of its circular shape. Because the shape of the ascending aorta in the cCTA axial view is roughly a circle but its size can vary over a wide range for different patients, multiscale circularshape priors are used to search for the best matching circular object in each CT slice, guided by the Hausdorff distance (HD) as the matching indicator. The location of the aorta is identified by finding the minimum HD in the heart region over the set of multiscale circular priors. An adaptive region growing method is then used to extend the above initially identified aorta down to the aortic valves. The origins at the aortic sinus are finally identified by a morphological gray level top-hat operation applied to the region-grown aorta with morphological structuring element designed for coronary arteries. For the 40 test cases, the aorta was correctly identified in 38 cases (95%). The aorta can be grown to the aortic root in 36 cases, and 36 LCA origins and 34 RCA origins can be identified within 10 mm of the locations marked by radiologists.

Modeling the survival kinetics of Salmonella in tree nuts for use in risk assessment.

PubMed

Santillana Farakos, Sofia M; Pouillot, Régis; Anderson, Nathan; Johnson, Rhoma; Son, Insook; Van Doren, Jane

2016-06-16

Salmonella has been shown to survive in tree nuts over long periods of time. This survival capacity and its variability are key elements for risk assessment of Salmonella in tree nuts. The aim of this study was to develop a mathematical model to predict survival of Salmonella in tree nuts at ambient storage temperatures that considers variability and uncertainty separately and can easily be incorporated into a risk assessment model. Data on Salmonella survival on raw almonds, pecans, pistachios and walnuts were collected from the peer reviewed literature. The Weibull model was chosen as the baseline model and various fixed effect and mixed effect models were fit to the data. The best model identified through statistical analysis testing was then used to develop a hierarchical Bayesian model. Salmonella in tree nuts showed slow declines at temperatures ranging from 21°C to 24°C. A high degree of variability in survival was observed across tree nut studies reported in the literature. Statistical analysis results indicated that the best applicable model was a mixed effect model that included a fixed and random variation of δ per tree nut (which is the time it takes for the first log10 reduction) and a fixed variation of ρ per tree nut (parameter which defines the shape of the curve). Higher estimated survival rates (δ) were obtained for Salmonella on pistachios, followed in decreasing order by pecans, almonds and walnuts. The posterior distributions obtained from Bayesian inference were used to estimate the variability in the log10 decrease levels in survival for each tree nut, and the uncertainty of these estimates. These modeled uncertainty and variability distributions of the estimates can be used to obtain a complete exposure assessment of Salmonella in tree nuts when including time-temperature parameters for storage and consumption data. The statistical approach presented in this study may be applied to any studies that aim to develop predictive models to be implemented in a probabilistic exposure assessment or a quantitative microbial risk assessment. Published by Elsevier B.V.

Unsupervised individual tree crown detection in high-resolution satellite imagery

DOE PAGES

Skurikhin, Alexei N.; McDowell, Nate G.; Middleton, Richard S.

2016-01-26

Rapidly and accurately detecting individual tree crowns in satellite imagery is a critical need for monitoring and characterizing forest resources. We present a two-stage semiautomated approach for detecting individual tree crowns using high spatial resolution (0.6 m) satellite imagery. First, active contours are used to recognize tree canopy areas in a normalized difference vegetation index image. Given the image areas corresponding to tree canopies, we then identify individual tree crowns as local extrema points in the Laplacian of Gaussian scale-space pyramid. The approach simultaneously detects tree crown centers and estimates tree crown sizes, parameters critical to multiple ecosystem models. Asmore » a demonstration, we used a ground validated, 0.6 m resolution QuickBird image of a sparse forest site. The two-stage approach produced a tree count estimate with an accuracy of 78% for a naturally regenerating forest with irregularly spaced trees, a success rate equivalent to or better than existing approaches. In addition, our approach detects tree canopy areas and individual tree crowns in an unsupervised manner and helps identify overlapping crowns. Furthermore, the method also demonstrates significant potential for further improvement.« less

Unsupervised individual tree crown detection in high-resolution satellite imagery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skurikhin, Alexei N.; McDowell, Nate G.; Middleton, Richard S.

Rapidly and accurately detecting individual tree crowns in satellite imagery is a critical need for monitoring and characterizing forest resources. We present a two-stage semiautomated approach for detecting individual tree crowns using high spatial resolution (0.6 m) satellite imagery. First, active contours are used to recognize tree canopy areas in a normalized difference vegetation index image. Given the image areas corresponding to tree canopies, we then identify individual tree crowns as local extrema points in the Laplacian of Gaussian scale-space pyramid. The approach simultaneously detects tree crown centers and estimates tree crown sizes, parameters critical to multiple ecosystem models. Asmore » a demonstration, we used a ground validated, 0.6 m resolution QuickBird image of a sparse forest site. The two-stage approach produced a tree count estimate with an accuracy of 78% for a naturally regenerating forest with irregularly spaced trees, a success rate equivalent to or better than existing approaches. In addition, our approach detects tree canopy areas and individual tree crowns in an unsupervised manner and helps identify overlapping crowns. Furthermore, the method also demonstrates significant potential for further improvement.« less

Product Support Manager Guidebook

DTIC Science & Technology

2011-04-01

package is being developed using supportability analysis concepts such as Failure Mode, Effects and Criticality Analysis (FMECA), Fault Tree Analysis ( FTA ...Analysis (LORA) Condition Based Maintenance + (CBM+) Fault Tree Analysis ( FTA ) Failure Mode, Effects, and Criticality Analysis (FMECA) Maintenance Task...Reporting and Corrective Action System (FRACAS), Fault Tree Analysis ( FTA ), Level of Repair Analysis (LORA), Maintenance Task Analysis (MTA

The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia

PubMed Central

Constable, Fiona E.; Nancarrow, Narelle; Rodoni, Brendan

2018-01-01

Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries. PMID:29562672

Tree nut allergens.

PubMed

Geiselhart, Sabine; Hoffmann-Sommergruber, Karin; Bublin, Merima

2018-04-18

Tree nuts are considered as part of a healthy diet due to their high nutritional quality. However, they are also a potent source of allergenic proteins inducing IgE mediated hypersensitivity often causing serious, life-threatening reactions. The reported prevalence of tree nut allergy is up to 4.9% worldwide. The general term "tree nuts" comprises a number of nuts, seeds, and drupes, derived from trees from different botanical families. For hazelnut and walnut several allergens have been identified which are already partly applied in component resolved diagnosis, while for other tree nuts such as macadamia, coconut, and Brazil nut only individual allergens were identified and data on additional allergenic proteins are missing. This review summarizes the current knowledge on tree nut allergens and describes their physicochemical and immunological characterization and clinical relevance. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Application of Failure Mode and Effect Analysis (FMEA), cause and effect analysis, and Pareto diagram in conjunction with HACCP to a corn curl manufacturing plant.

PubMed

Varzakas, Theodoros H; Arvanitoyannis, Ioannis S

2007-01-01

The Failure Mode and Effect Analysis (FMEA) model has been applied for the risk assessment of corn curl manufacturing. A tentative approach of FMEA application to the snacks industry was attempted in an effort to exclude the presence of GMOs in the final product. This is of crucial importance both from the ethics and the legislation (Regulations EC 1829/2003; EC 1830/2003; Directive EC 18/2001) point of view. The Preliminary Hazard Analysis and the Fault Tree Analysis were used to analyze and predict the occurring failure modes in a food chain system (corn curls processing plant), based on the functions, characteristics, and/or interactions of the ingredients or the processes, upon which the system depends. Critical Control points have been identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram, and the fishbone diagram). Finally, Pareto diagrams were employed towards the optimization of GMOs detection potential of FMEA.

Analysis of yellow "fat" deposits on Inuit boots.

PubMed

Edwards, Howell G M; Stern, Ben; Burgio, Lucia; Kite, Marion

2009-08-01

Irregular residues of a yellow deposit that was assumed to be seal fat used for waterproofing were observed in the creases of the outer surface of a pair of Inuit boots from Arctic Canada. A sample of this deposit detached from one of these areas on these boots was examined initially by FT-Raman microscopy, from which interesting and rather surprising results demanded further analysis using FT-IR and GC-MS. The non-destructive Raman spectroscopic analysis yielded spectra which indicated the presence of a tree resin from the Pinaceae sp. The Raman spectra were also characteristic of a well-preserved keratotic protein and indicative of adherent skin. Subsequent FT-IR spectroscopic analysis supported the attribution of a Pinaceae resin to the yellow deposit. GC-MS analysis of the same deposits identified the presence of pimaric, sandaracopimaric, dehydroabietic and abietic acids, all indicative of an aged Pinaceae resin. These results confirmed that the Inuit people had access to tree resins which they probably used as a waterproofing agent.

Risk profiles for weight gain among postmenopausal women: A classification and regression tree analysis approach

USDA-ARS?s Scientific Manuscript database

Risk factors for obesity and weight gain are typically evaluated individually while "adjusting for" the influence of other confounding factors, and few studies, if any, have created risk profiles by clustering risk factors. We identified subgroups of postmenopausal women homogeneous in their cluster...

Pesticides in Urban Multiunit Dwellings: Hazard IdentificationUsing Classification and Regression Tree (CART) Analysis

EPA Science Inventory

Many units in public housing or other low-income urban dwellings may have elevated pesticide residues, given recurring infestation, but it would be logistically and economically infeasible to sample a large number of units to identify highly exposed households to design interven...

Optimal ranking regime analysis of TreeFlow dendrohydrological reconstructions

USDA-ARS?s Scientific Manuscript database

The Optimal Ranking Regime (ORR) method was used to identify 6-100 year time windows containing significant ranking sequences in 55 western U.S. streamflow reconstructions, and reconstructions of the level of the Great Salt Lake and San Francisco Bay salinity during 1500-2007. The method’s ability t...

Application of fault tree approach for the causation mechanism of urban haze in Beijing--Considering the risk events related with exhausts of coal combustion.

PubMed

Huang, Weiqing; Fan, Hongbo; Qiu, Yongfu; Cheng, Zhiyu; Qian, Yu

2016-02-15

Haze weather has become a serious environmental pollution problem which occurs in many Chinese cities. One of the most critical factors for the formation of haze weather is the exhausts of coal combustion, thus it is meaningful to figure out the causation mechanism between urban haze and the exhausts of coal combustion. Based on above considerations, the fault tree analysis (FAT) approach was employed for the causation mechanism of urban haze in Beijing by considering the risk events related with the exhausts of coal combustion for the first time. Using this approach, firstly the fault tree of the urban haze causation system connecting with coal combustion exhausts was established; consequently the risk events were discussed and identified; then, the minimal cut sets were successfully determined using Boolean algebra; finally, the structure, probability and critical importance degree analysis of the risk events were completed for the qualitative and quantitative assessment. The study results proved that the FTA was an effective and simple tool for the causation mechanism analysis and risk management of urban haze in China. Copyright © 2015 Elsevier B.V. All rights reserved.

Use of CHAID Decision Trees to Formulate Pathways for the Early Detection of Metabolic Syndrome in Young Adults

PubMed Central

Liu, Pei-Yang

2014-01-01

Metabolic syndrome (MetS) in young adults (age 20–39) is often undiagnosed. A simple screening tool using a surrogate measure might be invaluable in the early detection of MetS. Methods. A chi-squared automatic interaction detection (CHAID) decision tree analysis with waist circumference user-specified as the first level was used to detect MetS in young adults using data from the National Health and Nutrition Examination Survey (NHANES) 2009-2010 Cohort as a representative sample of the United States population (n = 745). Results. Twenty percent of the sample met the National Cholesterol Education Program Adult Treatment Panel III (NCEP) classification criteria for MetS. The user-specified CHAID model was compared to both CHAID model with no user-specified first level and logistic regression based model. This analysis identified waist circumference as a strong predictor in the MetS diagnosis. The accuracy of the final model with waist circumference user-specified as the first level was 92.3% with its ability to detect MetS at 71.8% which outperformed comparison models. Conclusions. Preliminary findings suggest that young adults at risk for MetS could be identified for further followup based on their waist circumference. Decision tree methods show promise for the development of a preliminary detection algorithm for MetS. PMID:24817904

Size-associated morphological variation in the red tree vole (Arborimus longicaudus)

Treesearch

Mark P. Miller; Eric D. Forsman; James K. Swingle; Stephanie A. Miller; Susan M. Haig

2010-01-01

We examined patterns of size-associated morphological variation within the Red Tree Vole (Arborimus longicaudus) for the purposes of 1) identifying differences between the Red Tree Vole and the Dusky Tree Vole (A. l. silvicola), a putative subspecies of the Red Tree Vole; and 2) examining spatial patterns of morphological...

Tree Hazards Recognition and Reduction in Recreation Sites

Treesearch

David W. Johnson

1981-01-01

Defective trees are potential hazards to people and property in recreation areas. Most reported tree failures within recreation sites in the Rocky Mountain Region occur in lodgepole pine. Defective root systems account for the greatest percentage of failures. External indicators of defects are used to identify trees that may fail. Some tree species, particularly aspen...

Deriving pathway maps from automated text analysis using a grammar-based approach.

PubMed

Olsson, Björn; Gawronska, Barbara; Erlendsson, Björn

2006-04-01

We demonstrate how automated text analysis can be used to support the large-scale analysis of metabolic and regulatory pathways by deriving pathway maps from textual descriptions found in the scientific literature. The main assumption is that correct syntactic analysis combined with domain-specific heuristics provides a good basis for relation extraction. Our method uses an algorithm that searches through the syntactic trees produced by a parser based on a Referent Grammar formalism, identifies relations mentioned in the sentence, and classifies them with respect to their semantic class and epistemic status (facts, counterfactuals, hypotheses). The semantic categories used in the classification are based on the relation set used in KEGG (Kyoto Encyclopedia of Genes and Genomes), so that pathway maps using KEGG notation can be automatically generated. We present the current version of the relation extraction algorithm and an evaluation based on a corpus of abstracts obtained from PubMed. The results indicate that the method is able to combine a reasonable coverage with high accuracy. We found that 61% of all sentences were parsed, and 97% of the parse trees were judged to be correct. The extraction algorithm was tested on a sample of 300 parse trees and was found to produce correct extractions in 90.5% of the cases.

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution.

PubMed

Francis, Andrew; Moulton, Vincent

2018-06-07

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are quite limited in terms of the complexity of the networks that are considered. In this paper, by introducing an alternative probabilistic model for evolution along a network that is based on some ground-breaking work by Thatte for pedigrees, we are able to obtain an identifiability result for a much larger class of phylogenetic networks (essentially the class of so-called tree-child networks). To prove our main theorem, we derive some new results for identifying tree-child networks combinatorially, and then adapt some techniques developed by Thatte for pedigrees to show that our combinatorial results imply identifiability in the probabilistic setting. We hope that the introduction of our new model for networks could lead to new approaches to reliably construct phylogenetic networks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distributed Contour Trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morozov, Dmitriy; Weber, Gunther H.

2014-03-31

Topological techniques provide robust tools for data analysis. They are used, for example, for feature extraction, for data de-noising, and for comparison of data sets. This chapter concerns contour trees, a topological descriptor that records the connectivity of the isosurfaces of scalar functions. These trees are fundamental to analysis and visualization of physical phenomena modeled by real-valued measurements. We study the parallel analysis of contour trees. After describing a particular representation of a contour tree, called local{global representation, we illustrate how di erent problems that rely on contour trees can be solved in parallel with minimal communication.

Analyzing tree cores to detect petroleum hydrocarbon-contaminated groundwater at a former landfill site in the community of Happy Valley-Goose Bay, eastern Canadian subarctic.

PubMed

Fonkwe, Merline L D; Trapp, Stefan

2016-08-01

This research examines the feasibility of analyzing tree cores to detect benzene, toluene, ethylbenzene, and m, p, o-xylene (BTEX) compounds and methyl tertiary-butyl ether (MTBE) in groundwater in eastern Canada subarctic environments, using a former landfill site in the remote community of Happy Valley-Goose Bay, Labrador. Petroleum hydrocarbon contamination at the landfill site is the result of environmentally unsound pre-1990s disposal of households and industrial solid wastes. Tree cores were taken from trembling aspen, black spruce, and white birch and analyzed by headspace-gas chromatography-mass spectrometry. BTEX compounds were detected in tree cores, corroborating known groundwater contamination. A zone of anomalously high concentrations of total BTEX constituents was identified and recommended for monitoring by groundwater wells. Tree cores collected outside the landfill site at a local control area suggest the migration of contaminants off-site. Tree species exhibit different concentrations of BTEX constituents, indicating selective uptake and accumulation. Toluene in wood exhibited the highest concentrations, which may also be due to endogenous production. Meanwhile, MTBE was not found in the tree cores and is considered to be absent in the groundwater. The results demonstrate that tree-core analysis can be useful for detecting anomalous concentrations of petroleum hydrocarbons, such as BTEX compounds, in subarctic sites with shallow unconfined aquifers and permeable soils. This method can therefore aid in the proper management of contamination during landfill operations and after site closures.

Application of Failure Mode and Effect Analysis (FMEA) and cause and effect analysis in conjunction with ISO 22000 to a snails (Helix aspersa) processing plant; A case study.

PubMed

Arvanitoyannis, Ioannis S; Varzakas, Theodoros H

2009-08-01

Failure Mode and Effect Analysis (FMEA) has been applied for the risk assessment of snails manufacturing. A tentative approach of FMEA application to the snails industry was attempted in conjunction with ISO 22000. Preliminary Hazard Analysis was used to analyze and predict the occurring failure modes in a food chain system (snails processing plant), based on the functions, characteristics, and/or interactions of the ingredients or the processes, upon which the system depends. Critical Control points have been identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram, and fishbone diagram). In this work a comparison of ISO22000 analysis with HACCP is carried out over snails processing and packaging. However, the main emphasis was put on the quantification of risk assessment by determining the RPN per identified processing hazard. Sterilization of tins, bioaccumulation of heavy metals, packaging of shells and poisonous mushrooms, were the processes identified as the ones with the highest RPN (280, 240, 147, 144, respectively) and corrective actions were undertaken. Following the application of corrective actions, a second calculation of RPN values was carried out leading to considerably lower values (below the upper acceptable limit of 130). It is noteworthy that the application of Ishikawa (Cause and Effect or Tree diagram) led to converging results thus corroborating the validity of conclusions derived from risk assessment and FMEA. Therefore, the incorporation of FMEA analysis within the ISO22000 system of a snails processing industry is considered imperative.

Identification of Chinese medicine syndromes in persistent insomnia associated with major depressive disorder: a latent tree analysis.

PubMed

Yeung, Wing-Fai; Chung, Ka-Fai; Zhang, Nevin Lian-Wen; Zhang, Shi Ping; Yung, Kam-Ping; Chen, Pei-Xian; Ho, Yan-Yee

2016-01-01

Chinese medicine (CM) syndrome (zheng) differentiation is based on the co-occurrence of CM manifestation profiles, such as signs and symptoms, and pulse and tongue features. Insomnia is a symptom that frequently occurs in major depressive disorder despite adequate antidepressant treatment. This study aims to identify co-occurrence patterns in participants with persistent insomnia and major depressive disorder from clinical feature data using latent tree analysis, and to compare the latent variables with relevant CM syndromes. One hundred and forty-two participants with persistent insomnia and a history of major depressive disorder completed a standardized checklist (the Chinese Medicine Insomnia Symptom Checklist) specially developed for CM syndrome classification of insomnia. The checklist covers symptoms and signs, including tongue and pulse features. The clinical features assessed by the checklist were analyzed using Lantern software. CM practitioners with relevant experience compared the clinical feature variables under each latent variable with reference to relevant CM syndromes, based on a previous review of CM syndromes. The symptom data were analyzed to build the latent tree model and the model with the highest Bayes information criterion score was regarded as the best model. This model contained 18 latent variables, each of which divided participants into two clusters. Six clusters represented more than 50 % of the sample. The clinical feature co-occurrence patterns of these six clusters were interpreted as the CM syndromes Liver qi stagnation transforming into fire, Liver fire flaming upward, Stomach disharmony, Hyperactivity of fire due to yin deficiency, Heart-kidney noninteraction, and Qi deficiency of the heart and gallbladder. The clinical feature variables that contributed significant cumulative information coverage (at least 95 %) were identified. Latent tree model analysis on a sample of depressed participants with insomnia revealed 13 clinical feature co-occurrence patterns, four mutual-exclusion patterns, and one pattern with a single clinical feature variable.

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

PubMed Central

Meerow, Alan W.; Noblick, Larry; Borrone, James W.; Couvreur, Thomas L. P.; Mauro-Herrera, Margarita; Hahn, William J.; Kuhn, David N.; Nakamura, Kyoko; Oleas, Nora H.; Schnell, Raymond J.

2009-01-01

Background The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the “abominable mysteries” of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. Methodology/Principal Findings We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. Conclusions/Significance This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family. PMID:19806212

Oxygen and carbon stable isotopes in coast redwood tree rings respond to spring and summer climate signals

NASA Astrophysics Data System (ADS)

Johnstone, James A.; Roden, John S.; Dawson, Todd E.

2013-12-01

variability in the oxygen and carbon isotope composition of tree ring cellulose was investigated in coast redwood (Sequoia sempervirens) from three sites in coastal Northern California. Middle and late wood samples from annual tree rings were compared to regional climate indices and gridded ocean-atmosphere fields for the years 1952-2003. The strongest climate-isotope relationship (r = 0.72) was found with summer (June-September) daily maximum temperature and middle wood δ13, which also responds positively to coastal sea surface temperature and negatively to summer low cloud frequency. Late wood δ18O reflects a balance between 18O-enriched summer fog drip and depleted summer rainwater, while a combined analysis of late wood δ18O and δ13C revealed sensitivity to the sign of summer precipitation anomalies. Empirical orthogonal function analysis of regional summer climate indices and coast redwood stable isotopes identified multivariate isotopic responses to summer fog and drought that correspond to atmospheric circulation anomalies over the NE Pacific and NW U.S. The presence of regional climate signals in coast redwood stable isotope composition, consistent with known mechanistic processes and prior studies, offers the potential for high-resolution paleoclimate reconstructions of the California current system from this long-lived tree species.

Environmental Biomonitoring of Cr and As in Shallow Groundwater: Do Red Oak Trees Preserve Long-Term Records of Contaminant Loading?

NASA Astrophysics Data System (ADS)

Shailer, M.; Brabander, D.

2005-05-01

The use of dendrochemical analysis has been shown to be a valuable, although controversial, tool in monitoring historical trends in trace metal deposition and mobilization in groundwater and sediments. Neutron activation analysis (NAA) is one method that has been used to determine annual dendrochemical patterns in tree rings. The use of NAA may also provide a practical tool for revealing sub-annual differences in metal concentrations between earlywood and latewood. In a variety of geochemical settings, Cr and As can be mobile in the groundwater-root environment and are subsequently taken up by trees and stored in xylem tissues specifically associated with groundwater transport. For the purposes of determining historical patterns in Cr and As bioavailability at a Woburn, MA, superfund site along the Aberjona River, Quercus rubra (red oak) sectioned tree rings were analyzed. Sub-annual dendrochemical analyses were used to identify different As and Cr loading pathways in oak stem wood. A sixty-year record of [As] and [Cr] in stem wood was obtained, and results suggest seasonally dependent correlations with Aberjona River flow and with pumping rates for a municipal well in close proximity to the sampling location. These two hydrological pathways likely dominate in providing a flux of dissolved As and Cr into oak stem wood.

Properly placed shade trees reduce summertime electricity bills in Sacramento, California

Treesearch

Geoffery H. Donovan; David R. Butry

2009-01-01

The discovery that shade trees can reduce home cooling costs is hardly surprising. Anybody who has sat under a tree on a warm summer day understands the shade benefit of trees. However, quantifying the effect a shade tree has on home energy use and carbon footprint, and identifying the optimal location for a shade tree, is less straightforward. Past studies that have...

Spatial Characteristics of Tree Diameter Distributions in a Temperate Old-Growth Forest

PubMed Central

Zhao, Xiuhai; von Gadow, Klaus

2013-01-01

This contribution identifies spatial characteristics of tree diameter in a temperate forest in north-eastern China, based on a fully censused observational study area covering 500×600 m. Mark correlation analysis with three null hypothesis models was used to determine departure from expectations at different neighborhood distances. Tree positions are clumped at all investigated scales in all 37 studied species, while the diameters of most species are spatially negatively correlated, especially at short distances. Interestingly, all three cases showing short-distance attraction of dbh marks are associated with light-demanding shrub species. The short-distance attraction of dbh marks indicates spatially aggregated cohorts of stems of similar size. The percentage of species showing significant dbh suppression peaked at a 4 m distance under the heterogeneous Poisson model. At scales exceeding the peak distance, the percentage of species showing significant dbh suppression decreases sharply with increasing distances. The evidence from this large observational study shows that some of the variation of the spatial characteristics of tree diameters is related variations of topography and soil chemistry. However, an obvious interpretation of this result is still lacking. Thus, removing competitors surrounding the target trees is an effective way to avoid neighboring competition effects reducing the growth of valuable target trees in forest management practice. PMID:23527066

Spatial characteristics of tree diameter distributions in a temperate old-growth forest.

PubMed

Zhang, Chunyu; Wei, Yanbo; Zhao, Xiuhai; von Gadow, Klaus

2013-01-01

This contribution identifies spatial characteristics of tree diameter in a temperate forest in north-eastern China, based on a fully censused observational study area covering 500×600 m. Mark correlation analysis with three null hypothesis models was used to determine departure from expectations at different neighborhood distances. Tree positions are clumped at all investigated scales in all 37 studied species, while the diameters of most species are spatially negatively correlated, especially at short distances. Interestingly, all three cases showing short-distance attraction of dbh marks are associated with light-demanding shrub species. The short-distance attraction of dbh marks indicates spatially aggregated cohorts of stems of similar size. The percentage of species showing significant dbh suppression peaked at a 4 m distance under the heterogeneous Poisson model. At scales exceeding the peak distance, the percentage of species showing significant dbh suppression decreases sharply with increasing distances. The evidence from this large observational study shows that some of the variation of the spatial characteristics of tree diameters is related variations of topography and soil chemistry. However, an obvious interpretation of this result is still lacking. Thus, removing competitors surrounding the target trees is an effective way to avoid neighboring competition effects reducing the growth of valuable target trees in forest management practice.

Bark flammability as a fire-response trait for subalpine trees

PubMed Central

Frejaville, Thibaut; Curt, Thomas; Carcaillet, Christopher

2013-01-01

Relationships between the flammability properties of a given plant and its chances of survival after a fire still remain unknown. We hypothesize that the bark flammability of a tree reduces the potential for tree survival following surface fires, and that if tree resistance to fire is provided by a thick insulating bark, the latter must be few flammable. We test, on subalpine tree species, the relationship between the flammability of bark and its insulating ability, identifies the biological traits that determine bark flammability, and assesses their relative susceptibility to surface fires from their bark properties. The experimental set of burning properties was analyzed by Principal Component Analysis to assess the bark flammability. Bark insulating ability was expressed by the critical time to cambium kill computed from bark thickness. Log-linear regressions indicated that bark flammability varies with the bark thickness and the density of wood under bark and that the most flammable barks have poor insulating ability. Susceptibility to surface fires increases from gymnosperm to angiosperm subalpine trees. The co-dominant subalpine species Larix decidua (Mill.) and Pinus cembra (L.) exhibit large differences in both flammability and insulating ability of the bark that should partly explain their contrasted responses to fires in the past. PMID:24324473

Ergonomics aspects of tree-planting using 'multipot' technology.

PubMed

Giguère, D; Bélanger, R; Gauthier, J M; Larue, C

1993-08-01

The highlights of a descriptive study on the ergonomics and occupational health and safety aspects of tree-planting in Québec are presented. The study was planned to consider the most representative geographical sites, planting technologies, and planting organizations. Semi-directed interviews were made with a mixed group of 48 male and female tree-planters and physiological measurements were made on four male planters. Tools and other equipment were also examined. An analysis of the work identified the main elements of the planting cycle, and the high cardiac rate in the working planters was related more to his manual transportation of seedlings and travel on rough paths than to planting per se. A tree-planter will typically travel 2.4 km carrying 16.8 kg of material and equipment in order to plant an average of 1245 seedlings daily. One out of two interviewed planters reported having a work-related accident or incident during his or her lifetime planting career. The body parts reported most frequently injured were the lower extremities (knee, foot, ankle), the skin, the eyes, and the wrist. Recommendations on the development of appropriate tools and footwear for tree-planters and for further research on repetitive strain injury induced by tree-planting have been made.

tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

PubMed Central

Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

2014-01-01

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

Linking physiological processes with mangrove forest structure: phosphorus deficiency limits canopy development, hydraulic conductivity and photosynthetic carbon gain in dwarf Rhizophora mangle.

PubMed

Lovelock, Catherine E; Ball, Marilyn C; Choat, Brendan; Engelbrecht, Bettina M J; Holbrook, N Michelle; Feller, Ilka C

2006-05-01

Spatial gradients in mangrove tree height in barrier islands of Belize are associated with nutrient deficiency and sustained flooding in the absence of a salinity gradient. While nutrient deficiency is likely to affect many parameters, here we show that addition of phosphorus (P) to dwarf mangroves stimulated increases in diameters of xylem vessels, area of conductive xylem tissue and leaf area index (LAI) of the canopy. These changes in structure were consistent with related changes in function, as addition of P also increased hydraulic conductivity (Ks), stomatal conductance and photosynthetic assimilation rates to the same levels measured in taller trees fringing the seaward margin of the mangrove. Increased xylem vessel size and corresponding enhancements in stem hydraulic conductivity in P fertilized dwarf trees came at the cost of enhanced mid-day loss of hydraulic conductivity and was associated with decreased assimilation rates in the afternoon. Analysis of trait plasticity identifies hydraulic properties of trees as more plastic than those of leaf structural and physiological characteristics, implying that hydraulic properties are key in controlling growth in mangroves. Alleviation of P deficiency, which released trees from hydraulic limitations, reduced the structural and functional distinctions between dwarf and taller fringing tree forms of Rhizophora mangle.

Structural modeling and analysis of an effluent treatment process for electroplating--a graph theoretic approach.

PubMed

Kumar, Abhishek; Clement, Shibu; Agrawal, V P

2010-07-15

An attempt is made to address a few ecological and environment issues by developing different structural models for effluent treatment system for electroplating. The effluent treatment system is defined with the help of different subsystems contributing to waste minimization. Hierarchical tree and block diagram showing all possible interactions among subsystems are proposed. These non-mathematical diagrams are converted into mathematical models for design improvement, analysis, comparison, storage retrieval and commercially off-the-shelf purchases of different subsystems. This is achieved by developing graph theoretic model, matrix models and variable permanent function model. Analysis is carried out by permanent function, hierarchical tree and block diagram methods. Storage and retrieval is done using matrix models. The methodology is illustrated with the help of an example. Benefits to the electroplaters/end user are identified. 2010 Elsevier B.V. All rights reserved.

Try Fault Tree Analysis, a Step-by-Step Way to Improve Organization Development.

ERIC Educational Resources Information Center

Spitzer, Dean

1980-01-01

Fault Tree Analysis, a systems safety engineering technology used to analyze organizational systems, is described. Explains the use of logic gates to represent the relationship between failure events, qualitative analysis, quantitative analysis, and effective use of Fault Tree Analysis. (CT)

Application of the FTA and ETA Method for Gas Hazard Identification for the Performance of Safety Systems in the Industrial Department

NASA Astrophysics Data System (ADS)

Ignac-Nowicka, Jolanta

2018-03-01

The paper analyzes the conditions of safe use of industrial gas systems and factors influencing gas hazards. Typical gas installation and its basic features have been characterized. The results of gas threat analysis in an industrial enterprise using FTA error tree method and ETA event tree method are presented. Compares selected methods of identifying hazards gas industry with respect to the scope of their use. The paper presents an analysis of two exemplary hazards: an industrial gas catastrophe (FTA) and an explosive gas explosion (ETA). In both cases, technical risks and human errors (human factor) were taken into account. The cause-effect relationships of hazards and their causes are presented in the form of diagrams in the drawings.

Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum.

PubMed

Wang, Wei; Xia, Minxuan; Chen, Jie; Deng, Fenni; Yuan, Rui; Zhang, Xiaopei; Shen, Fafu

2016-12-01

The data presented in this paper is supporting the research article "Genome-Wide Analysis of Superoxide Dismutase Gene Family in Gossypium raimondii and G. arboreum" [1]. In this data article, we present phylogenetic tree showing dichotomy with two different clusters of SODs inferred by the Bayesian method of MrBayes (version 3.2.4), "Bayesian phylogenetic inference under mixed models" [2], Ramachandran plots of G. raimondii and G. arboreum SODs, the protein sequence used to generate 3D sructure of proteins and the template accession via SWISS-MODEL server, "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information." [3] and motif sequences of SODs identified by InterProScan (version 4.8) with the Pfam database, "Pfam: the protein families database" [4].

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem

PubMed Central

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation. PMID:28603535

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem.

PubMed

Chen, Yun; Niu, Shuai; Li, Peikun; Jia, Hongru; Wang, Hailiang; Ye, Yongzhong; Yuan, Zhiliang

2017-01-01

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m 2 along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation.

The utility of a classificatory decision tree approach to assist clinical differentiation of melancholic and non-melancholic depression.

PubMed

Parker, G; McCraw, S; Hadzi-Pavlovic, D

2015-07-15

Studies suggest that differentiating melancholic from non-melancholic depressive disorders is advanced by use of illness course as well as symptom variables but, in practice, potentially differentiating variables are generally positioned as having equal value. Judging that differentiating features are more likely to vary in their signal intensity, we sought to determine the number of features required to effect differentiation and their hierarchical order. The 24-item clinician-rated Sydney Melancholia Prototype Index (SMPI-CR) was completed for 364 unipolar depressed patients. The sample was divided into two cohorts according to the recruitment period. An RPART classification tree analysis identified the most discriminating SMPI items in the development sample of 197 patients, and examined the sensitivity and specificity of the diagnostic decisions, then sought to replicate findings in a validation sample of 169 patients. Independent analyses of putative SMPI items identified only seven items as required to discriminate those with clinically-diagnosed melancholic or non-melancholic depression when the conditions were examined separately. An RPART analysis considering differentiation of melancholic and non-melancholic depression in the total samples retained five of those items in the classification tree, three of which were non-symptom items, and with 92% sensitivity and 80% specificity in the development sample. This reduced item set showed 93% sensitivity and 82% specificity in the validation sample. Our clinical judgment of melancholic or non-melancholic depression may not correspond with the clinical logic employed by other clinicians. Only five SMPI items were required to derive a succinct and efficient decision tree, comprising high sensitivity and specificity in differentiating melancholic and non-melancholic depression. Current study findings provide an empirical model that could enrich clinicians׳ approach to differentiating melancholic and non-melancholic depression. Copyright © 2015 Elsevier B.V. All rights reserved.

Seasonal Variation of Carbon Metabolism in the Cambial Zone of Eucalyptus grandis

PubMed Central

Budzinski, Ilara G. F.; Moon, David H.; Lindén, Pernilla; Moritz, Thomas; Labate, Carlos A.

2016-01-01

Eucalyptus species are the most widely hardwood planted in the world. It is one of the successful examples of commercial forestry plantation in Brazil and other tropical and subtropical countries. The tree is valued for its rapid growth, adaptability and wood quality. Wood formation is the result of cumulative annual activity of the vascular cambium. This cambial activity is generally related to the alternation of cold and warm, and/or dry and rainy seasons. Efforts have focused on analysis of cambial zone in response to seasonal variations in trees from temperate zones. However, little is known about the molecular changes triggered by seasonal variations in trees from tropical countries. In this work we attempted to establish a global view of seasonal alterations in the cambial zone of Eucalyptus grandis Hill ex Maiden, emphasizing changes occurring in the carbon metabolism. Using transcripts, proteomics and metabolomics we analyzed the tissues harvested in summer-wet and winter-dry seasons. Based on proteomics analysis, 70 proteins that changed in abundance were successfully identified. Transcripts for some of these proteins were analyzed and similar expression patterns were observed. We identified 19 metabolites differentially abundant. Our results suggest a differential reconfiguration of carbon partioning in E. grandis cambial zone. During summer, pyruvate is primarily metabolized via ethanolic fermentation, possibly to regenerate NAD+ for glycolytic ATP production and cellular maintenance. However, in winter there seems to be a metabolic change and we found that some sugars were highly abundant. Our results revealed a dynamic change in E. grandis cambial zone due to seasonality and highlight the importance of glycolysis and ethanolic fermentation for energy generation and maintenance in Eucalyptus, a fast growing tree. PMID:27446160

A voxel-based technique to estimate the volume of trees from terrestrial laser scanner data

NASA Astrophysics Data System (ADS)

Bienert, A.; Hess, C.; Maas, H.-G.; von Oheimb, G.

2014-06-01

The precise determination of the volume of standing trees is very important for ecological and economical considerations in forestry. If terrestrial laser scanner data are available, a simple approach for volume determination is given by allocating points into a voxel structure and subsequently counting the filled voxels. Generally, this method will overestimate the volume. The paper presents an improved algorithm to estimate the wood volume of trees using a voxel-based method which will correct for the overestimation. After voxel space transformation, each voxel which contains points is reduced to the volume of its surrounding bounding box. In a next step, occluded (inner stem) voxels are identified by a neighbourhood analysis sweeping in the X and Y direction of each filled voxel. Finally, the wood volume of the tree is composed by the sum of the bounding box volumes of the outer voxels and the volume of all occluded inner voxels. Scan data sets from several young Norway maple trees (Acer platanoides) were used to analyse the algorithm. Therefore, the scanned trees as well as their representing point clouds were separated in different components (stem, branches) to make a meaningful comparison. Two reference measurements were performed for validation: A direct wood volume measurement by placing the tree components into a water tank, and a frustum calculation of small trunk segments by measuring the radii along the trunk. Overall, the results show slightly underestimated volumes (-0.3% for a probe of 13 trees) with a RMSE of 11.6% for the individual tree volume calculated with the new approach.

Review: Evaluation of Foot-and-Mouth Disease Control Using Fault Tree Analysis.

PubMed

Isoda, N; Kadohira, M; Sekiguchi, S; Schuppers, M; Stärk, K D C

2015-06-01

An outbreak of foot-and-mouth disease (FMD) causes huge economic losses and animal welfare problems. Although much can be learnt from past FMD outbreaks, several countries are not satisfied with their degree of contingency planning and aiming at more assurance that their control measures will be effective. The purpose of the present article was to develop a generic fault tree framework for the control of an FMD outbreak as a basis for systematic improvement and refinement of control activities and general preparedness. Fault trees are typically used in engineering to document pathways that can lead to an undesired event, that is, ineffective FMD control. The fault tree method allows risk managers to identify immature parts of the control system and to analyse the events or steps that will most probably delay rapid and effective disease control during a real outbreak. The present developed fault tree is generic and can be tailored to fit the specific needs of countries. For instance, the specific fault tree for the 2001 FMD outbreak in the UK was refined based on control weaknesses discussed in peer-reviewed articles. Furthermore, the specific fault tree based on the 2001 outbreak was applied to the subsequent FMD outbreak in 2007 to assess the refinement of control measures following the earlier, major outbreak. The FMD fault tree can assist risk managers to develop more refined and adequate control activities against FMD outbreaks and to find optimum strategies for rapid control. Further application using the current tree will be one of the basic measures for FMD control worldwide. © 2013 Blackwell Verlag GmbH.

Current and Potential Tree Locations in Tree Line Ecotone of Changbai Mountains, Northeast China: The Controlling Effects of Topography

PubMed Central

Zong, Shengwei; Wu, Zhengfang; Xu, Jiawei; Li, Ming; Gao, Xiaofeng; He, Hongshi; Du, Haibo; Wang, Lei

2014-01-01

Tree line ecotone in the Changbai Mountains has undergone large changes in the past decades. Tree locations show variations on the four sides of the mountains, especially on the northern and western sides, which has not been fully explained. Previous studies attributed such variations to the variations in temperature. However, in this study, we hypothesized that topographic controls were responsible for causing the variations in the tree locations in tree line ecotone of the Changbai Mountains. To test the hypothesis, we used IKONOS images and WorldView-1 image to identify the tree locations and developed a logistic regression model using topographical variables to identify the dominant controls of the tree locations. The results showed that aspect, wetness, and slope were dominant controls for tree locations on western side of the mountains, whereas altitude, SPI, and aspect were the dominant factors on northern side. The upmost altitude a tree can currently reach was 2140 m asl on the northern side and 2060 m asl on western side. The model predicted results showed that habitats above the current tree line on the both sides were available for trees. Tree recruitments under the current tree line may take advantage of the available habitats at higher elevations based on the current tree location. Our research confirmed the controlling effects of topography on the tree locations in the tree line ecotone of Changbai Mountains and suggested that it was essential to assess the tree response to topography in the research of tree line ecotone. PMID:25170918

Current and potential tree locations in tree line ecotone of Changbai Mountains, Northeast China: the controlling effects of topography.

PubMed

Zong, Shengwei; Wu, Zhengfang; Xu, Jiawei; Li, Ming; Gao, Xiaofeng; He, Hongshi; Du, Haibo; Wang, Lei

2014-01-01

Tree line ecotone in the Changbai Mountains has undergone large changes in the past decades. Tree locations show variations on the four sides of the mountains, especially on the northern and western sides, which has not been fully explained. Previous studies attributed such variations to the variations in temperature. However, in this study, we hypothesized that topographic controls were responsible for causing the variations in the tree locations in tree line ecotone of the Changbai Mountains. To test the hypothesis, we used IKONOS images and WorldView-1 image to identify the tree locations and developed a logistic regression model using topographical variables to identify the dominant controls of the tree locations. The results showed that aspect, wetness, and slope were dominant controls for tree locations on western side of the mountains, whereas altitude, SPI, and aspect were the dominant factors on northern side. The upmost altitude a tree can currently reach was 2140 m asl on the northern side and 2060 m asl on western side. The model predicted results showed that habitats above the current tree line on the both sides were available for trees. Tree recruitments under the current tree line may take advantage of the available habitats at higher elevations based on the current tree location. Our research confirmed the controlling effects of topography on the tree locations in the tree line ecotone of Changbai Mountains and suggested that it was essential to assess the tree response to topography in the research of tree line ecotone.

Unveiling Members of Colletotrichum acutatum Species Complex Causing Colletotrichum Leaf Disease of Hevea brasiliensis in Sri Lanka.

PubMed

Hunupolagama, D M; Chandrasekharan, N V; Wijesundera, W S S; Kathriarachchi, H S; Fernando, T H P S; Wijesundera, R L C

2017-06-01

Colletotrichum is an important fungal genus with great diversity, which causes anthracnose of a variety of crop plants including rubber trees. Colletotrichum acutatum and Colletotrichum gloeosporioides have been identified as the major causative agents of Colletotrichum leaf disease of rubber trees in Sri Lanka based on morphology, pathogenicity, and the analysis of internally transcribed spacer sequences of the nuclear ribosomal DNA. This study has been conducted to investigate the members of the C. acutatum species complex causing rubber leaf disease using a morphological and multi gene approach. For the first time in Sri Lanka, Colletotrichum simmondsii, Colletotrichum laticiphilum, Colletotrichum nymphaeae, and Colletotrichum citri have been identified as causative agents of Colletotrichum leaf disease in addition to C. acutatum s. str. Among them, C. simmondsii has been recognized as the major causative agent.

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

PubMed Central

Rangiah, Kannan; Mahesh, HB; Rajamani, Anantharamanan; Shirke, Meghana D.; Russiachand, Heikham; Loganathan, Ramya Malarini; Shankara Lingu, Chandana; Siddappa, Shilpa; Ramamurthy, Aishwarya; Sathyanarayana, BN

2015-01-01

Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways. PMID:26290780

A six hundred-year annual minimum temperature history for the central Tibetan Plateau derived from tree-ring width series

NASA Astrophysics Data System (ADS)

He, Minhui; Yang, Bao; Datsenko, Nina M.

2014-08-01

The recent unprecedented warming found in different regions has aroused much attention in the past years. How temperature has really changed on the Tibetan Plateau (TP) remains unknown since very limited high-resolution temperature series can be found over this region, where large areas of snow and ice exist. Herein, we develop two Juniperus tibetica Kom. tree-ring width chronologies from different elevations. We found that the two tree-ring series only share high-frequency variability. Correlation, response function and partial correlation analysis indicate that prior year annual (January-December) minimum temperature is most responsible for the higher belt juniper radial growth, while more or less precipitation signal is contained by the tree-ring width chronology at the lower belt and is thus excluded from further analysis. The tree growth-climate model accounted for 40 % of the total variance in actual temperature during the common period 1957-2010. The detected temperature signal is further robustly verified by other results. Consequently, a six century long annual minimum temperature history was firstly recovered for the Yushu region, central TP. Interestingly, the rapid warming trend during the past five decades is identified as a significant cold phase in the context of the past 600 years. The recovered temperature series reflects low-frequency variability consistent with other temperature reconstructions over the whole TP region. Furthermore, the present recovered temperature series is associated with the Asian monsoon strength on decadal to multidecadal scales over the past 600 years.

Identification of microRNAs differentially expressed involved in male flower development.

PubMed

Wang, Zhengjia; Huang, Jianqin; Sun, Zhichao; Zheng, Bingsong

2015-03-01

Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.

Health and disease phenotyping in old age using a cluster network analysis.

PubMed

Valenzuela, Jesus Felix; Monterola, Christopher; Tong, Victor Joo Chuan; Ng, Tze Pin; Larbi, Anis

2017-11-15

Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree. We show, by way of a correspondence analysis between the two sets of clusters, that they correspond to coarse-grained and fine-grained structure of the network relationships. The clusters obtained from the minimum spanning tree mapped to various conceptual domains and corresponded to physiological and syndromic states. Hierarchical ordering of these clusters identified six common themes based on interactions with physiological systems and common underlying substrates of age-associated morbidity and disease chronicity, functional disability, and quality of life. These findings provide a starting point for indepth analyses of ageing that incorporate immunologic, metabolomic and proteomic biomarkers, and ultimately offer low-level-based typologies of healthy and unhealthy ageing.

A mid-layer model for human reliability analysis : understanding the cognitive causes of human failure events.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Song-Hua; Chang, James Y. H.; Boring,Ronald L.

2010-03-01

The Office of Nuclear Regulatory Research (RES) at the US Nuclear Regulatory Commission (USNRC) is sponsoring work in response to a Staff Requirements Memorandum (SRM) directing an effort to establish a single human reliability analysis (HRA) method for the agency or guidance for the use of multiple methods. As part of this effort an attempt to develop a comprehensive HRA qualitative approach is being pursued. This paper presents a draft of the method's middle layer, a part of the qualitative analysis phase that links failure mechanisms to performance shaping factors. Starting with a Crew Response Tree (CRT) that has identifiedmore » human failure events, analysts identify potential failure mechanisms using the mid-layer model. The mid-layer model presented in this paper traces the identification of the failure mechanisms using the Information-Diagnosis/Decision-Action (IDA) model and cognitive models from the psychological literature. Each failure mechanism is grouped according to a phase of IDA. Under each phase of IDA, the cognitive models help identify the relevant performance shaping factors for the failure mechanism. The use of IDA and cognitive models can be traced through fault trees, which provide a detailed complement to the CRT.« less

CHRONIC IRRADIATION OF SCOTS PINE TREES (PINUS SYLVESTRIS) IN THE CHERNOBYL EXCLUSION ZONE: DOSIMETRY AND RADIOBIOLOGICAL EFFECTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farfan, E.; Jannik, T.

To identify effects of chronic internal and external radiation exposure for components of terrestrial ecosystems, a comprehensive study of Scots pine trees in the Chernobyl Exclusion Zone was performed. The experimental plan included over 1,100 young trees (up to 20 years old) selected from areas with varying levels of radioactive contamination. These pine trees were planted after the 1986 Chernobyl Nuclear Power Plant accident mainly to prevent radionuclide resuspension and soil erosion. For each tree, the major morphological parameters and radioactive contamination values were identified. Cytological analyses were performed for selected trees representing all dose rate ranges. A specially developedmore » dosimetric model capable of taking into account radiation from the incorporated radionuclides in the trees was developed for the apical meristem. The calculated dose rates for the trees in the study varied within three orders of magnitude, from close to background values in the control area (about 5 mGy y{sup -1}) to approximately 7 Gy y{sup -1} in the Red Forest area located in the immediate vicinity of the Chernobyl Nuclear Power Plant site. Dose rate/effect relationships for morphological changes and cytogenetic defects were identified and correlations for radiation effects occurring on the morphological and cellular level were established.« less

Magnetic Resonance Imaging Measures of Brain Structure to Predict Antidepressant Treatment Outcome in Major Depressive Disorder.

PubMed

Korgaonkar, Mayuresh S; Rekshan, William; Gordon, Evian; Rush, A John; Williams, Leanne M; Blasey, Christine; Grieve, Stuart M

2015-01-01

Less than 50% of patients with Major Depressive Disorder (MDD) reach symptomatic remission with their initial antidepressant medication (ADM). There are currently no objective measures with which to reliably predict which individuals will achieve remission to ADMs. 157 participants with MDD from the International Study to Predict Optimized Treatment in Depression (iSPOT-D) underwent baseline MRIs and completed eight weeks of treatment with escitalopram, sertraline or venlafaxine-ER. A score at week 8 of 7 or less on the 17 item Hamilton Rating Scale for Depression defined remission. Receiver Operator Characteristics (ROC) analysis using the first 50% participants was performed to define decision trees of baseline MRI volumetric and connectivity (fractional anisotropy) measures that differentiated non-remitters from remitters with maximal sensitivity and specificity. These decision trees were tested for replication in the remaining participants. Overall, 35% of all participants achieved remission. ROC analyses identified two decision trees that predicted a high probability of non-remission and that were replicated: 1. Left middle frontal volume < 14 · 8 mL & right angular gyrus volume > 6 · 3 mL identified 55% of non-remitters with 85% accuracy; and 2. Fractional anisotropy values in the left cingulum bundle < 0 · 63, right superior fronto-occipital fasciculus < 0 · 54 and right superior longitudinal fasciculus < 0 · 50 identified 15% of the non-remitters with 84% accuracy. All participants who met criteria for both decision trees were correctly identified as non-remitters. Pretreatment MRI measures seem to reliably identify a subset of patients who do not remit with a first step medication that includes one of these commonly used medications. Findings are consistent with a neuroanatomical basis for non-remission in depressed patients. Brain Resource Ltd is the sponsor for the iSPOT-D study (NCT00693849).

[Phylogenetic and diversity analysis of Acidithiobacillus spp. based on 16S rRNA and RubisCO genes homologues].

PubMed

Liu, Minrui; Lin, Pengwu; Qi, Xing'e; Ni, Yongqing

2016-04-14

The purpose of the study was to reveal geographic region-related Acidithiobacillus spp. distribution and allopatric speciation. Phylogenetic and diversity analysis was done to expand our knowledge on microbial phylogeography, diversity-maintaining mechanisms and molecular biogeography. We amplified 16S rRNA gene and RubisCO genes to construct corresponding phylogenetic trees based on the sequence homology and analyzed genetic diversity of Acidithiobacillus spp.. Thirty-five strains were isolated from three different regions in China (Yunnan, Hubei, Xinjiang). The whole isolates were classified into five groups. Four strains were identified as A. ferrivorans, six as A. ferridurans, YNTR4-15 Leptspirillum ferrooxidans and HBDY3-31 as Leptospirillum ferrodiazotrophum. The remaining strains were identified as A. ferrooxidans. Analysis of cbbL and cbbM genes sequences of representative 26 strains indicated that cbbL gene of 19 were two copies (cbbL1 and cbbL2) and 7 possessed only cbbL1. cbbM gene was single copy. In nucleotide-based trees, cbbL1 gene sequences of strains were separated into three sequence types, and the cbbL2 was similar to cbbL1 with three types. Codon bias of RubisCO genes was not obvious in Acidithiobacillus spp.. Strains isolated from three different regions in China indicated a great genetic diversity in Acidithiobacillus spp. and their 16S rRNA/RubisCO genes sequence was of significant difference. Phylogenetic tree based on 16S rRNA genes and RubisCO genes was different in Acidithiobacillus spp..

Stain Associated with Nails in Trees on Permanent Plots

Treesearch

Charles B. Briscoe; Benton H. Box

1959-01-01

In studies involving the measurement and subsequent remeasurement of trees, such as CFI plots or siliviculture research plots, the trees are commonly identified by metal tags fastened to the trees by means of nails. In 1957 a study was begun to determine whether this practice would lead to dregrade or scalable defect in the trees.

Utility of tree crown condition indicators to predict tree survival using remeasured Forest Inventory and Analysis data

Treesearch

Randall S. Morin; Jim Steinman; KaDonna C. Randolph

2012-01-01

The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during surveys of Forest Inventory and Analysis (FIA) Phase 3 (P3) plots since 1999. In this study, remeasured data from 39,357 trees in the northern United States were used to assess the probability of survival among various tree species using the...

Application of Infrared and Raman Spectroscopy for the Identification of Disease Resistant Trees.

PubMed

Conrad, Anna O; Bonello, Pierluigi

2015-01-01

New approaches for identifying disease resistant trees are needed as the incidence of diseases caused by non-native and invasive pathogens increases. These approaches must be rapid, reliable, cost-effective, and should have the potential to be adapted for high-throughput screening or phenotyping. Within the context of trees and tree diseases, we summarize vibrational spectroscopic and chemometric methods that have been used to distinguish between groups of trees which vary in disease susceptibility or other important characteristics based on chemical fingerprint data. We also provide specific examples from the literature of where these approaches have been used successfully. Finally, we discuss future application of these approaches for wide-scale screening and phenotyping efforts aimed at identifying disease resistant trees and managing forest diseases.

A comparative critical study between FMEA and FTA risk analysis methods

NASA Astrophysics Data System (ADS)

Cristea, G.; Constantinescu, DM

2017-10-01

Today there is used an overwhelming number of different risk analyses techniques with acronyms such as: FMEA (Failure Modes and Effects Analysis) and its extension FMECA (Failure Mode, Effects, and Criticality Analysis), DRBFM (Design Review by Failure Mode), FTA (Fault Tree Analysis) and and its extension ETA (Event Tree Analysis), HAZOP (Hazard & Operability Studies), HACCP (Hazard Analysis and Critical Control Points) and What-if/Checklist. However, the most used analysis techniques in the mechanical and electrical industry are FMEA and FTA. In FMEA, which is an inductive method, information about the consequences and effects of the failures is usually collected through interviews with experienced people, and with different knowledge i.e., cross-functional groups. The FMEA is used to capture potential failures/risks & impacts and prioritize them on a numeric scale called Risk Priority Number (RPN) which ranges from 1 to 1000. FTA is a deductive method i.e., a general system state is decomposed into chains of more basic events of components. The logical interrelationship of how such basic events depend on and affect each other is often described analytically in a reliability structure which can be visualized as a tree. Both methods are very time-consuming to be applied thoroughly, and this is why it is oftenly not done so. As a consequence possible failure modes may not be identified. To address these shortcomings, it is proposed to use a combination of FTA and FMEA.

Using acoustic analysis to presort warp-prone ponderosa pine 2 by 4s before kiln-drying

Treesearch

Xiping Wang; William T. Simpson

2006-01-01

This study evaluated the potential of acoustic analysis as presorting criteria to identify warp-prone boards before kiln-drying. Dimension lumber, 38 by 89 mm (nominal 2 by 4 in.) and 2.44 m (8 it) long, sawn from open-grown small-diameter ponderosa pine trees, was acoustically tested lengthwise at green condition. Three acoustic properties (acoustic speed, rate of...

Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.).

PubMed

Malviya, N; Gupta, S; Singh, V K; Yadav, M K; Bisht, N C; Sarangi, B K; Yadav, D

2015-02-01

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

Patterns and Drivers of Scattered Tree Loss in Agricultural Landscapes: Orchard Meadows in Germany (1968-2009)

PubMed Central

Plieninger, Tobias; Levers, Christian; Mantel, Martin; Costa, Augusta; Schaich, Harald; Kuemmerle, Tobias

2015-01-01

Scattered trees support high levels of farmland biodiversity and ecosystem services in agricultural landscapes, but they are threatened by agricultural intensification, urbanization, and land abandonment. This study aimed to map and quantify the decline of orchard meadows (scattered fruit trees of high nature conservation value) for a region in Southwestern Germany for the 1968 2009 period and to identify the driving forces of this decline. We derived orchard meadow loss from 1968 and 2009 aerial images and used a boosted regression trees modelling framework to assess the relative importance of 18 environmental, demographic, and socio-economic variables to test five alternative hypothesis explaining orchard meadow loss. We found that orchard meadow loss occurred in flatter areas, in areas where smaller plot sizes and fragmented orchard meadows prevailed, and in areas near settlements and infrastructure. The analysis did not confirm that orchard meadow loss was higher in areas where agricultural intensification was stronger and in areas of lower implementation levels of conservation policies. Our results demonstrated that the influential drivers of orchard meadow loss were those that reduce economic profitability and increase opportunity costs for orchards, providing incentives for converting orchard meadows to other, more profitable land uses. These insights could be taken up by local- and regional-level conservation policies to identify the sites of persistent orchard meadows in agricultural landscapes that would be prioritized in conservation efforts. PMID:25932914

Identification of triacylglycerol using automated annotation of high resolution multistage mass spectral trees.

PubMed

Wang, Xiupin; Peng, Qingzhi; Li, Peiwu; Zhang, Qi; Ding, Xiaoxia; Zhang, Wen; Zhang, Liangxiao

2016-10-12

High complexity of identification for non-target triacylglycerols (TAGs) is a major challenge in lipidomics analysis. To identify non-target TAGs, a powerful tool named accurate MS(n) spectrometry generating so-called ion trees is used. In this paper, we presented a technique for efficient structural elucidation of TAGs on MS(n) spectral trees produced by LTQ Orbitrap MS(n), which was implemented as an open source software package, or TIT. The TIT software was used to support automatic annotation of non-target TAGs on MS(n) ion trees from a self-built fragment ion database. This database includes 19108 simulate TAG molecules from a random combination of fatty acids and corresponding 500582 self-built multistage fragment ions (MS ≤ 3). Our software can identify TAGs using a "stage-by-stage elimination" strategy. By utilizing the MS(1) accurate mass and referenced RKMD, the TIT software can discriminate unique elemental composition candidates. The regiospecific isomers of fatty acyl chains will be distinguished using MS(2) and MS(3) fragment spectra. We applied the algorithm to the selection of 45 TAG standards and demonstrated that the molecular ions could be 100% correctly assigned. Therefore, the TIT software could be applied to TAG identification in complex biological samples such as mouse plasma extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

A simultaneous characterization and uncertainty analysis of thermal conductivity and diffusivity of bio-insulate material "Palm date Wood" obtained from a periodic method

NASA Astrophysics Data System (ADS)

Tlijani, M.; Ben Younes, R.; Durastanti, J. F.; Boudenne, A.

2010-11-01

A periodic method is used to determine simultaneously both thermal conductivity and diffusivity of various insulate materials at room temperature. The sample is placed between two metallic plates and temperature modulation is applied on the front side of one of the metallic plates. The temperature at the front and rear sides of both plates is measured and the experimental transfer function is calculated. The theoretical thermal heat transfer function is calculated by the quadripole method. Thermal conductivity and diffusivity are simultaneously identified from both real and imaginary parts of the experimental transfer function. The thermophysical parameters of several wood scale samples obtained from palm wood trees and common trees with unknown thermal properties (E) with different thicknesses were studied. The value identified for the thermal conductivity 0.03 Wm-1 K-1 compared with different insulate solid material such as glass, glass-wool and PVC is much better and close to the air conductivity, It allowed us to consider the wood scale extracted from palm wood trees, bio and renewable material as good heat insulator aiming in the future as a use for lightness applications, insulating or as a reinforcement in a given matrix. These potentialities still unknown are stengthened by the enormous quantity of such kind of wood gathered annually from palm trees and considered as wastes.

Estimating global distribution of boreal, temperate, and tropical tree plant functional types using clustering techniques

NASA Astrophysics Data System (ADS)

Wang, Audrey; Price, David T.

2007-03-01

A simple integrated algorithm was developed to relate global climatology to distributions of tree plant functional types (PFT). Multivariate cluster analysis was performed to analyze the statistical homogeneity of the climate space occupied by individual tree PFTs. Forested regions identified from the satellite-based GLC2000 classification were separated into tropical, temperate, and boreal sub-PFTs for use in the Canadian Terrestrial Ecosystem Model (CTEM). Global data sets of monthly minimum temperature, growing degree days, an index of climatic moisture, and estimated PFT cover fractions were then used as variables in the cluster analysis. The statistical results for individual PFT clusters were found consistent with other global-scale classifications of dominant vegetation. As an improvement of the quantification of the climatic limitations on PFT distributions, the results also demonstrated overlapping of PFT cluster boundaries that reflected vegetation transitions, for example, between tropical and temperate biomes. The resulting global database should provide a better basis for simulating the interaction of climate change and terrestrial ecosystem dynamics using global vegetation models.

Effects of lung disease on the three-dimensional structure and air flow pattern in the human airway tree

NASA Astrophysics Data System (ADS)

van de Moortele, Tristan; Nemes, Andras; Wendt, Christine; Coletti, Filippo

2016-11-01

The morphological features of the airway tree directly affect the air flow features during breathing, which determines the gas exchange and inhaled particle transport. Lung disease, Chronic Obstructive Pulmonary Disease (COPD) in this study, affects the structural features of the lungs, which in turn negatively affects the air flow through the airways. Here bronchial tree air volume geometries are segmented from Computed Tomography (CT) scans of healthy and diseased subjects. Geometrical analysis of the airway centerlines and corresponding cross-sectional areas provide insight into the specific effects of COPD on the airway structure. These geometries are also used to 3D print anatomically accurate, patient specific flow models. Three-component, three-dimensional velocity fields within these models are acquired using Magnetic Resonance Imaging (MRI). The three-dimensional flow fields provide insight into the change in flow patterns and features. Additionally, particle trajectories are determined using the velocity fields, to identify the fate of therapeutic and harmful inhaled aerosols. Correlation between disease-specific and patient-specific anatomical features with dysfunctional airflow patterns can be achieved by combining geometrical and flow analysis.

Warming-Induced Decline of Picea crassifolia Growth in the Qilian Mountains in Recent Decades.

PubMed

Yu, Li; Huang, Lei; Shao, Xuemei; Xiao, Fengjing; Wilmking, Martin; Zhang, Yongxiang

2015-01-01

Warming-induced drought has widely affected forest dynamics in most places of the northern hemisphere. In this study, we assessed how climate warming has affected Picea crassifolia (Qinghai spruce) forests using tree growth-climate relationships and the normalized difference vegetation index (NDVI) along the Qilian Mountains, northeastern Tibet Plateau (the main range of Picea crassifolia). Based on the analysis on trees radial growth data from the upper tree line and the regional NDVI data, we identified a pervasive growth decline in recent decades, most likely caused by warming-induced droughts. The drought stress on Picea crassifolia radial growth were expanding from northeast to southwest and the favorable moisture conditions for tree growth were retreating along the identical direction in the study area over the last half century. Compared to the historical drought stress on tree radial growth in the 1920s, recent warming-induced droughts display a longer-lasting stress with a broader spatial distribution on regional forest growth. If the recent warming continues without the effective moisture increasing, then a notable challenge is developed for Picea crassifolia in the Qilian Mountains. Elaborate forest management is necessary to counteract the future risk of climate change effects in this region.

Changes in Vegetation Reflect Changes in the Mammoth Mountain and Long Valley Caldera Hydrothermal System

NASA Astrophysics Data System (ADS)

Murphy, F.; Diefenbach, A. K.; Evans, W.; Hurwitz, S.

2013-12-01

We examined aerial photographs of the area near Mammoth Lakes, CA taken from 1951 to the present, with the goal of determining if visible changes in vegetation might reflect changes in the upflow of gas or heat through the soil zone. Such changes could be related to magmatic intrusion, the development of geothermal resources, groundwater pumping, earthquakes, or to natural changes in the hydrothermal flow system. We examined the area near Horseshoe Lake at the southern base of Mammoth Mountain where diffuse emissions of carbon dioxide created extensive tree-kill in the 1990s. Analysis of photographs acquired in 1951 suggests that tree density in this area was lower than its surroundings at the time. Whether the low-density tree cover identified in the photographs indicates some lasting effects of a previous episode of tree mortality needs further investigation. We also examine possible effects of geothermal energy production at Casa Diablo that began operation in 1985 on vegetation along the western part of the resurgent dome of Long Valley Caldera. Previous studies have correlated tree-kill in this area with increased steam upflow from the hydrothermal system.

Dendrometric measurements reveal stages leading to tree mortality in a semiarid pine forest

NASA Astrophysics Data System (ADS)

Tatarinov, Fyodor; Preisler, Yakir; Klein, Tamir; Rotenberg, Eyal; Yakir, Dan

2017-04-01

Increasing frequency and intensity of climatic extreme events, such as droughts may lead to increasing vulnerability of forests, especially in semi-arid regions. In the spring of 2016 mortality was observed among trees used for sap flow (SF) and dendrometry measurements in the semi-arid Fluxnet pine forest site of Yatir in Israel (280mm annual mean precipitation). This was accompanied by bark-beetle attack, and with visual drying of needles starting in April 2016. Comparative analysis of dendrometry and sap flux (SF) measurements in 31 trees of which 7 died and 24 survived permitted identification of the stages leading to tree mortality. Distinction between dying and surviving trees was identified in the dendrometric measurements from Nov. 2015, about five months before visual mortality signs: First, clear decline in diameter (DBH) was observed in all dying trees, whereas DBH of living trees remained constant until the first rain in January 2016 followed by growth. Second, the diurnal patterns in DBH showed a gradual shift of the diurnal DBH maximum from noon-time to early morning from the summer of 2015 to the spring of 2016 in surviving trees, whereas in dying trees it remained stable around noontime. Third, the diurnal swelling/shrinkage dynamics, assumed to reflect water use and storage dynamics, showed clear decline in magnitude, down to near zero, in the dying trees while regular daily cycle continued in the surviving trees. In September 2015 Shoot measurements showed midnight minimum of leaf water potential, lower than in living trees (-4.5 vs. -3.6 MPa respectively). Sap flow measurements were not sufficiently sensitive during the non-active season (fall and early winter) and indicated changes only after the first rain in January 2016. At this time, SF showed dramatic increase in SF with typical midday maximum in the surviving trees, whereas in dying trees SF remained low and irregular. The results show that indicators of mortality can be detected at least 5 months before visual signs are observed, and demonstrate the interacting effects of carbon economy (growth) and tree water management (radial water movement and storage) on the development of mortality in Aleppo pine trees.

Hydrochemical analysis of groundwater using a tree-based model

NASA Astrophysics Data System (ADS)

Litaor, M. Iggy; Brielmann, H.; Reichmann, O.; Shenker, M.

2010-06-01

SummaryHydrochemical indices are commonly used to ascertain aquifer characteristics, salinity problems, anthropogenic inputs and resource management, among others. This study was conducted to test the applicability of a binary decision tree model to aquifer evaluation using hydrochemical indices as input. The main advantage of the tree-based model compared to other commonly used statistical procedures such as cluster and factor analyses is the ability to classify groundwater samples with assigned probability and the reduction of a large data set into a few significant variables without creating new factors. We tested the model using data sets collected from headwater springs of the Jordan River, Israel. The model evaluation consisted of several levels of complexity, from simple separation between the calcium-magnesium-bicarbonate water type of karstic aquifers to the more challenging separation of calcium-sodium-bicarbonate water type flowing through perched and regional basaltic aquifers. In all cases, the model assigned measures for goodness of fit in the form of misclassification errors and singled out the most significant variable in the analysis. The model proceeded through a sequence of partitions providing insight into different possible pathways and changing lithology. The model results were extremely useful in constraining the interpretation of geological heterogeneity and constructing a conceptual flow model for a given aquifer. The tree model clearly identified the hydrochemical indices that were excluded from the analysis, thus providing information that can lead to a decrease in the number of routinely analyzed variables and a significant reduction in laboratory cost.

A cross-sectional study for predicting tail biting risk in pig farms using classification and regression tree analysis.

PubMed

Scollo, Annalisa; Gottardo, Flaviana; Contiero, Barbara; Edwards, Sandra A

2017-10-01

Tail biting in pigs has been an identified behavioural, welfare and economic problem for decades, and requires appropriate but sometimes difficult on-farm interventions. The aim of the paper is to introduce the Classification and Regression Tree (CRT) methodologies to develop a tool for prevention of acute tail biting lesions in pigs on-farm. A sample of 60 commercial farms rearing heavy pigs were involved; an on-farm visit and an interview with the farmer collected data on general management, herd health, disease prevention, climate control, feeding and production traits. Results suggest a value for the CRT analysis in managing the risk factors behind tail biting on a farm-specific level, showing 86.7% sensitivity for the Classification Tree and a correlation of 0.7 between observed and predicted prevalence of tail biting obtained with the Regression Tree. CRT analysis showed five main variables (stocking density, ammonia levels, number of pigs per stockman, type of floor and timeliness in feed supply) as critical predictors of acute tail biting lesions, which demonstrate different importance in different farms subgroups. The model might have reliable and practical applications for the support and implementation of tail biting prevention interventions, especially in case of subgroups of pigs with higher risk, helping farmers and veterinarians to assess the risk in their own farm and to manage their predisposing variables in order to reduce acute tail biting lesions. Copyright © 2017 Elsevier B.V. All rights reserved.

Transcriptomic analysis of Prunus domestica undergoing hypersensitive response to plum pox virus infection.

PubMed

Rodamilans, Bernardo; San León, David; Mühlberger, Louisa; Candresse, Thierry; Neumüller, Michael; Oliveros, Juan Carlos; García, Juan Antonio

2014-01-01

Plum pox virus (PPV) infects Prunus trees around the globe, posing serious fruit production problems and causing severe economic losses. One variety of Prunus domestica, named 'Jojo', develops a hypersensitive response to viral infection. Here we compared infected and non-infected samples using next-generation RNA sequencing to characterize the genetic complexity of the viral population in infected samples and to identify genes involved in development of the resistance response. Analysis of viral reads from the infected samples allowed reconstruction of a PPV-D consensus sequence. De novo reconstruction showed a second viral isolate of the PPV-Rec strain. RNA-seq analysis of PPV-infected 'Jojo' trees identified 2,234 and 786 unigenes that were significantly up- or downregulated, respectively (false discovery rate; FDR≤0.01). Expression of genes associated with defense was generally enhanced, while expression of those related to photosynthesis was repressed. Of the total of 3,020 differentially expressed unigenes, 154 were characterized as potential resistance genes, 10 of which were included in the NBS-LRR type. Given their possible role in plant defense, we selected 75 additional unigenes as candidates for further study. The combination of next-generation sequencing and a Prunus variety that develops a hypersensitive response to PPV infection provided an opportunity to study the factors involved in this plant defense mechanism. Transcriptomic analysis presented an overview of the changes that occur during PPV infection as a whole, and identified candidates suitable for further functional characterization.

Solar and Climate Variation Relationships Analyzed from Chile Tree Ring Width Time Series (1587 - 1994 A.D.)

NASA Astrophysics Data System (ADS)

Rigozo, Nr; Nordemann, Djr; Faria, Hh; Echer, E.; Vieira, Lea; Prestes, A.

This work presents a study of the relations between solar and climate variations during the last four centuries by spectral analysis of tree ring index and sunspot number time series. Trees used for this study were Pilgerodendron cupressoides from Glaciar Pio XI, in Chile. The spectral analysis of tree ring index shows that 11, 22 and 80 year periodicities of the solar cycle were present in this tree ring data with 0.95 confidence level. This result suggests a solar modulation of climate variations, as recorded by the tree ring growth. Short-term variations, between 2 - 7 years, are also present in tree ring data. Therefore spectral analysis clearly shows that both, solar and climate factors, are recorded in the tree ring data.

STRIDE: Species Tree Root Inference from Gene Duplication Events.

PubMed

Emms, David M; Kelly, Steven

2017-12-01

The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards.

PubMed

Blom, Mozes P K; Bragg, Jason G; Potter, Sally; Moritz, Craig

2017-05-01

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference. [Coalescence; concatenation; Cryptoblepharus; exon capture; gene tree; phylogenomics; species tree.]. © The authors 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Large-scale protein analysis of European beech trees following four vegetation periods of twice ambient ozone exposure.

PubMed

Kerner, René; Delgado-Eckert, Edgar; Ernst, Dieter; Dupuy, Jean-William; Grams, Thorsten E E; Barbro Winkler, J; Lindermayr, Christian; Müller-Starck, Gerhard

2014-09-23

In the present study, we performed a large-scale protein analysis based on 2-DE DIGE to examine the effects of ozone on the leaves of juvenile European beech (Fagus sylvatica L.), one of the most important deciduous tree species in Central Europe. To this end, beech trees were grown under field conditions and subjected to ambient and twice ambient ozone concentrations during the vegetation periods of four consecutive years. The twice ambient ozone concentration altered the abundance of 237 protein spots, which showed relative ratios higher than 30% compared to the ambient control trees. A total of 74 protein spots were subjected to mass spectrometry identification (LC-MS/MS), followed by homology-driven searches. The differentially expressed proteins participate in key biological processes including the Calvin cycle and photosynthesis, carbon metabolism, defense- and stress-related responses, detoxification mechanisms, protein folding and degradation, and mechanisms involved in senescence. The ozone-induced responses provide evidence of a changing carbon metabolism and counteraction against increased levels of reactive oxygen species. This study provides useful information on how European beech, an economically and ecologically important tree species, reacts on the molecular level to increased ozone concentrations expected in the near future. The main emphasis in the present study was placed on identifying differentially abundant proteins after long-term ozone exposure under climatically realistic settings, rather than short-term responses or reactions under laboratory conditions. Additionally, using nursery-grown beech trees, we took into account the natural genotypic variation of this species. As such, the results presented here provide information on molecular responses to ozone in an experimental plant system at very close to natural conditions. Furthermore, this proteomic approach was supported by previous studies on the present experiment. Ultimately, the combination of this proteomic approach with several approaches including transcriptomics, analysis of non-structural carbohydrates, and morphological effects contributes to a more global picture of how beech trees react under increased ozone concentrations. Copyright © 2014. Published by Elsevier B.V.

Rating experiments in forestry: How much agreement is there in tree marking?

PubMed Central

Pallarés Ramos, Carlos; Kędziora, Wojciech; Haufe, Jens; Stoyan, Dietrich

2018-01-01

The process of selecting individual trees by humans for forest management purposes is the result of a plethora of factors and processes that are hard to disentangle. And yet in the past many textbooks and other publications have maintained that this selection leads to somewhat unanimous results. In this study, we analysed the data of 36 so-called marteloscope experiments from all over Britain, which are managed by the Ae Training Centre (Scotland, UK). Our objective was (1) to establish how much agreement there actually was when asking test persons (raters) to apply two different thinning methods, low and crown thinning. In addition we (2) were interested in understanding some of the processes leading to certain levels of agreement and in relationships between the agreement measures and characteristics of forest structure. Our analysis was based on multivariate statistics, particularly using Fleiss’ kappa. This was the first time that an analysis of rater behaviour was performed at such a large scale and it revealed that the general agreement in tree selection in Britain was only slight to fair, i.e. much lower than in medical experiments. The variability of selecting individual trees was considerable. We also found that agreement in tree selection was much stronger in low-thinning as opposed to crown-thinning experiments. As the latter is an important method of Continuous Cover Forestry and British forestry is increasingly adopting this forest management type, our results suggested that there is a need to provide more training. Interestingly the different levels of agreement as identified by Fleiss’ kappa could not be explained by measures of forest structure, however, the mean conformity number, a surrogate of Fleiss’ kappa, showed correlations and indicated that conformity increased with increasing complexity of tree stem diameter structure. PMID:29566076

Habitat characterization of western hoolock gibbons Hoolock hoolock by examining home range microhabitat use.

PubMed

Akers, Alice A; Anwarul Islam, Md; Nijman, Vincent

2013-10-01

Conserving a species depends on an understanding of its habitat requirements. Primatologists often characterize the habitat requirements of primates using macroscale population-based approaches relying on correlations between habitat attributes and population abundances between sites with varying levels of disturbance. This approach only works for species spread between several populations. The populations of some primates do not fulfill these criteria, forcing researchers to rely on individual-based (microscale) rather than population-based approaches for habitat characterization. We examined the reliability of using micro-scale habitat characterizations by studying the microhabitat preferences of a group of wild western hoolock gibbons (Hoolock hoolock) in order to compare our results to the habitat preferences of western hoolock gibbons identified during a macroscale study of populations across Bangladesh. We used stepwise discriminant analysis to differentiate between the areas of low, medium, and high usage based on microhabitat characteristics (tree species availability, altitude, canopy connection, distance from forest edge, and levels of human disturbance). The gibbons used interior forest habitat with low food tree availability most frequently for sleeping and socializing, and used edge habitat containing high food tree availability for medium periods for feeding. These results indicate that the gibbons prefer interior forest but are frequently forced to visit the forest edge to feed. Therefore, the optimal habitat would be interior forest away from human disturbance with high sleeping-tree and feeding-tree availability. These habitat preferences are consistent with the habitat attributes of Bangladesh's largest remaining western hoolock gibbon populations, which live in areas containing low agricultural encroachment and high food-tree availability. Microhabitat use studies can be used to characterize the habitat requirements of a species, but should include multiple scales of analysis wherever possible.

Looking at Leaves.

ERIC Educational Resources Information Center

Nature Study, 1998

1998-01-01

Presents a Project Learning Tree (PLT) activity that allows students to describe how leaf characteristics vary from tree to tree and how these characteristics can be used to identify trees. This lesson plan features a description of levels, skills, objectives, materials, enrichment activities, assessment strategies, and a listing of related PLT…

Extrinsic regime shifts drive abrupt changes in regeneration dynamics at upper treeline in the Rocky Mountains, U.S.A.

PubMed

Elliott, Grant P

2012-07-01

Given the widespread and often dramatic influence of climate change on terrestrial ecosystems, it is increasingly common for abrupt threshold changes to occur, yet explicitly testing for climate and ecological regime shifts is lacking in climatically sensitive upper treeline ecotones. In this study, quantitative evidence based on empirical data is provided to support the key role of extrinsic, climate-induced thresholds in governing the spatial and temporal patterns of tree establishment in these high-elevation environments. Dendroecological techniques were used to reconstruct a 420-year history of regeneration dynamics within upper treeline ecotones along a latitudinal gradient (approximately 44-35 degrees N) in the Rocky Mountains. Correlation analysis was used to assess the possible influence of minimum and maximum temperature indices and cool-season (November-April) precipitation on regional age-structure data. Regime-shift analysis was used to detect thresholds in tree establishment during the entire period of record (1580-2000), temperature variables significantly Correlated with establishment during the 20th century, and cool-season precipitation. Tree establishment was significantly correlated with minimum temperature during the spring (March-May) and cool season. Regime-shift analysis identified an abrupt increase in regional tree establishment in 1950 (1950-1954 age class). Coincident with this period was a shift toward reduced cool-season precipitation. The alignment of these climate conditions apparently triggered an abrupt increase in establishment that was unprecedented during the period of record. Two main findings emerge from this research that underscore the critical role of climate in governing regeneration dynamics within upper treeline ecotones. (1) Regional climate variability is capable of exceeding bioclimatic thresholds, thereby initiating synchronous and abrupt changes in the spatial and temporal patterns of tree establishment at broad regional scales. (2) The importance of climate parameters exceeding critical threshold values and triggering a regime shift in tree establishment appears to be contingent on the alignment of favorable temperature and moisture regimes. This research suggests that threshold changes in the climate system can fundamentally alter regeneration dynamics within upper treeline ecotones and, through the use of regime-shift analysis, reveals important climate-vegetation linkages.

Fault Tree Analysis: A Research Tool for Educational Planning. Technical Report No. 1.

ERIC Educational Resources Information Center

Alameda County School Dept., Hayward, CA. PACE Center.

This ESEA Title III report describes fault tree analysis and assesses its applicability to education. Fault tree analysis is an operations research tool which is designed to increase the probability of success in any system by analyzing the most likely modes of failure that could occur. A graphic portrayal, which has the form of a tree, is…

Delineating Tree Types in a Complex Tropical Forest Setting Using High Resolution Multispectral Satellite Imagery

NASA Astrophysics Data System (ADS)

Cross, M.

2016-12-01

An improved process for the identification of tree types from satellite imagery for tropical forests is needed for more accurate assessments of the impact of forests on the global climate. La Selva Biological Station in Costa Rica was the tropical forest area selected for this particular study. WorldView-3 imagery was utilized because of its high spatial, spectral and radiometric resolution, its availability, and its potential to differentiate species in a complex forest setting. The first-step was to establish confidence in the high spatial and high radiometric resolution imagery from WorldView-3 in delineating tree types within a complex forest setting. In achieving this goal, ASD field spectrometer data were collected of specific tree species to establish solid ground control within the study site. The spectrometer data were collected from the top of each specific tree canopy utilizing established towers located at La Selva Biological Station so as to match the near-nadir view of the WorldView-3 imagery. The ASD data was processed utilizing the spectral response functions for each of the WorldView-3 bands to convert the ASD data into a band specific reflectivity. This allowed direct comparison of the ASD spectrometer reflectance data to the WorldView-3 multispectral imagery. The WorldView-3 imagery was processed to surface reflectance using two standard atmospheric correction procedures and the proprietary DigitalGlobe Atmospheric Compensation (AComp) product. The most accurate correction process was identified through comparison to the spectrometer data collected. A series of statistical measures were then utilized to access the accuracy of the processed imagery and which imagery bands are best suited for tree type identification. From this analysis, a segmentation/classification process was performed to identify individual tree type locations within the study area. It is envisioned the results of this study will improve traditional forest classification processes, provide more accurate assessments of species density and distribution, facilitate a more accurate biomass estimate of the tropical forest which will impact the accuracy of tree carbon storage estimates, and ultimately assist in developing a better overall characterization of tropical rainforest dynamics.

Cone Analysis of Southern Pines - A Guidebook

Treesearch

D.L. Bramlett; E.W. Belcher; G.L. DeBarr; G.D. Hertel; Robert P. Karrfalt; C.W. Lantz; T. Miller; K.D. Ware; H.O. Yates

1977-01-01

Southern pine tree improvement programs require an ample supply of improved seeds, but productron from southern pine seed orchards has often been disappointing. If high productron is to be malntained yields must be monitored and causes of seed losses must be identified. Techniques for determining seed efficiency were first used for red pine, Pinus resinosa...

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Treesearch

G.A. Tuskan; S. DiFazio; S. Jansson; J. Bohlmann; I. Grigoriev; U. Hellsten; N. Putnam; S. Ralph; S. Rombauts; A. Salamov; J. Schein; L. Sterck; A. Aerts; R.R. Bhalerao; R.P. Bhalerao; D. Blaudez; W. Boerjan; A. Brun; A. Brunner; V. Busov; M. Campbell; J. Carlson; M. Chalot; J. Chapman; G.-L. Chen; D. Cooper; P.M. Coutinho; J. Couturier; S. Covert; Q. Cronk; R. Cunningham; J. Davis; S. Degroeve; A. Dejardin; C. dePamphilis; J. Detter; B. Dirks; U. Dubchak; S. Duplessis; J. Ehlting; B. Ellis; K. Gendler; D. Goodstein; M. Gribskov; J. Grimwood; A. Groover; L. Gunter; B. Hamberger; B. Heinze; Y. Helariutta; B. Henrissat; D. Holligan; R. Holt; W. Huang; N. Islam-Faridi; S. Jones; M. Jones-Rhoades; R. Jorgensen; C. Joshi; J. Kangasjarvi; J. Karlsson; C. Kelleher; R. Kirkpatrick; M. Kirst; A. Kohler; U. Kalluri; F. Larimer; J. Leebens-Mack; J.-C. Leple; P. Locascio; Y. Lou; S. Lucas; F. Martin; B. Montanini; C. Napoli; D.R. Nelson; C. Nelson; K. Nieminen; O. Nilsson; V. Pereda; G. Peter; R. Philippe; G. Pilate; A. Poliakov; J. Razumovskaya; P. Richardson; C. Rinaldi; K. Ritland; P. Rouze; D. Ryaboy; J. Schumtz; J. Schrader; B. Segerman; H. Shin; A. Siddiqui; F. Sterky; A. Terry; C.-J. Tsai; E. Uberbacher; P. Unneberg; J. Vahala; K. Wall; S. Wessler; G. Yang; T. Yin; C. Douglas; M. Marra; G. Sandberg; Y. Van de Peer; D. Rokhsar

2006-01-01

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs...

The development of spectro-signature indicators of root disease impacts on forest stands

NASA Technical Reports Server (NTRS)

Weber, F. P.; Wear, J. F.

1970-01-01

A field research program was begun in 1969 and intensified in 1970 on the physiology and biophysical responses of second-growth Douglas fir infected with root rot fungus. A double tramway system was suspended between three 100-foot instrument towers to carry sensors for measuring the energy response from above both healthy and infected trees. Processing and analysis was completed of airborne multispectral scanner imagery collected over the Wind River research area in 1969. Likelihood ratio processing of three-channel infrared data and Euclidean distance analysis of ten-channel spectrometer data did not identify incipient root rot infection outside the training sets. In all cases infected fir was misclassified as healthy fir. It was concluded from careful examination of physiological data that Poria root rot infection has little effect on water metabolism and energy exchange. What was identified was a low-grade stress that affects respiration and metabolism over long periods of time. This led to minor changes in the external physical symptoms of Poria-infected trees which was revealed only in the shortwave reflectance data.

AIS spectra of desert shrub canopies

NASA Technical Reports Server (NTRS)

Murray, R.; Isaacson, D. L.; Schrumpf, B. J.; Ripple, W. J.; Lewis, A. J.

1986-01-01

Airborne Imaging Spectrometer (AIS) data were collected 30 August 1985 from a desert shrub community in central Oregon. Spectra from artificial targets placed on the test site and from bare soil, big sagebrush (Artemesia tridentata wyomingensis), silver sagebrush (Artemesia cana bolander), and exposed volcanic rocks were studied. Spectral data from grating position 3 (tree mode) were selected from 25 ground positions for analysis by Principal Factor Analysis (PFA). In this grating position, as many as six factors were identified as significant in contributing to spectral structure. Channels 74 through 84 (tree mode) best characterized between-class differences. Other channels were identified as nondiscriminating and as associated with such errors as excessive atmospheric absorption and grating positin changes. The test site was relatively simple with the two species (A. tridentata and A. cana) representing nearly 95% of biomass and with only two mineral backgrounds, a montmorillonitic soil and volcanic rocks. If, as in this study, six factors of spectral structure can be extracted from a single grating position from data acquired over a simple vegetation community, then AIS data must be considered rich in information-gathering potential.

SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees.

PubMed

DeBlasio, Dan F; Wisecaver, Jennifer H

2016-01-01

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.

Propensity score estimation: machine learning and classification methods as alternatives to logistic regression

PubMed Central

Westreich, Daniel; Lessler, Justin; Funk, Michele Jonsson

2010-01-01

Summary Objective Propensity scores for the analysis of observational data are typically estimated using logistic regression. Our objective in this Review was to assess machine learning alternatives to logistic regression which may accomplish the same goals but with fewer assumptions or greater accuracy. Study Design and Setting We identified alternative methods for propensity score estimation and/or classification from the public health, biostatistics, discrete mathematics, and computer science literature, and evaluated these algorithms for applicability to the problem of propensity score estimation, potential advantages over logistic regression, and ease of use. Results We identified four techniques as alternatives to logistic regression: neural networks, support vector machines, decision trees (CART), and meta-classifiers (in particular, boosting). Conclusion While the assumptions of logistic regression are well understood, those assumptions are frequently ignored. All four alternatives have advantages and disadvantages compared with logistic regression. Boosting (meta-classifiers) and to a lesser extent decision trees (particularly CART) appear to be most promising for use in the context of propensity score analysis, but extensive simulation studies are needed to establish their utility in practice. PMID:20630332

A computational framework for prime implicants identification in noncoherent dynamic systems.

PubMed

Di Maio, Francesco; Baronchelli, Samuele; Zio, Enrico

2015-01-01

Dynamic reliability methods aim at complementing the capability of traditional static approaches (e.g., event trees [ETs] and fault trees [FTs]) by accounting for the system dynamic behavior and its interactions with the system state transition process. For this, the system dynamics is here described by a time-dependent model that includes the dependencies with the stochastic transition events. In this article, we present a novel computational framework for dynamic reliability analysis whose objectives are i) accounting for discrete stochastic transition events and ii) identifying the prime implicants (PIs) of the dynamic system. The framework entails adopting a multiple-valued logic (MVL) to consider stochastic transitions at discretized times. Then, PIs are originally identified by a differential evolution (DE) algorithm that looks for the optimal MVL solution of a covering problem formulated for MVL accident scenarios. For testing the feasibility of the framework, a dynamic noncoherent system composed of five components that can fail at discretized times has been analyzed, showing the applicability of the framework to practical cases. © 2014 Society for Risk Analysis.

Increased spruce tree growth in Central Europe since 1960s.

PubMed

Cienciala, Emil; Altman, Jan; Doležal, Jiří; Kopáček, Jiří; Štěpánek, Petr; Ståhl, Göran; Tumajer, Jan

2018-04-01

Tree growth response to recent environmental changes is of key interest for forest ecology. This study addressed the following questions with respect to Norway spruce (Picea abies, L. Karst.) in Central Europe: Has tree growth accelerated during the last five decades? What are the main environmental drivers of the observed tree radial stem growth and how much variability can be explained by them? Using a nationwide dendrochronological sampling of Norway spruce in the Czech Republic (1246 trees, 266 plots), novel regional tree-ring width chronologies for 40(±10)- and 60(±10)-year old trees were assembled, averaged across three elevation zones (break points at 500 and 700m). Correspondingly averaged drivers, including temperature, precipitation, nitrogen (N) deposition and ambient CO 2 concentration, were used in a general linear model (GLM) to analyze the contribution of these in explaining tree ring width variability for the period from 1961 to 2013. Spruce tree radial stem growth responded strongly to the changing environment in Central Europe during the period, with a mean tree ring width increase of 24 and 32% for the 40- and 60-year old trees, respectively. The indicative General Linear Model analysis identified CO 2 , precipitation during the vegetation season, spring air temperature (March-May) and N-deposition as the significant covariates of growth, with the latter including interactions with elevation zones. The regression models explained 57% and 55% of the variability in the two tree ring width chronologies, respectively. Growth response to N-deposition showed the highest variability along the elevation gradient with growth stimulation/limitation at sites below/above 700m. A strong sensitivity of stem growth to CO 2 was also indicated, suggesting that the effect of rising ambient CO 2 concentration (direct or indirect by increased water use efficiency) should be considered in analyses of long-term growth together with climatic factors and N-deposition. Copyright © 2017 Elsevier B.V. All rights reserved.

Application of ISO 22000 and Failure Mode and Effect Analysis (FMEA) for industrial processing of salmon: a case study.

PubMed

Arvanitoyannis, Ioannis S; Varzakas, Theodoros H

2008-05-01

The Failure Mode and Effect Analysis (FMEA) model was applied for risk assessment of salmon manufacturing. A tentative approach of FMEA application to the salmon industry was attempted in conjunction with ISO 22000. Preliminary Hazard Analysis was used to analyze and predict the occurring failure modes in a food chain system (salmon processing plant), based on the functions, characteristics, and/or interactions of the ingredients or the processes, upon which the system depends. Critical Control points were identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram and fishbone diagram). In this work, a comparison of ISO 22000 analysis with HACCP is carried out over salmon processing and packaging. However, the main emphasis was put on the quantification of risk assessment by determining the RPN per identified processing hazard. Fish receiving, casing/marking, blood removal, evisceration, filet-making cooling/freezing, and distribution were the processes identified as the ones with the highest RPN (252, 240, 210, 210, 210, 210, 200 respectively) and corrective actions were undertaken. After the application of corrective actions, a second calculation of RPN values was carried out resulting in substantially lower values (below the upper acceptable limit of 130). It is noteworthy that the application of Ishikawa (Cause and Effect or Tree diagram) led to converging results thus corroborating the validity of conclusions derived from risk assessment and FMEA. Therefore, the incorporation of FMEA analysis within the ISO 22000 system of a salmon processing industry is anticipated to prove advantageous to industrialists, state food inspectors, and consumers.

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach.

PubMed

Ghadie, Mohamed A; Japkowicz, Nathalie; Perkins, Theodore J

2015-08-15

Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. tperkins@ohri.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories.

PubMed

Knowles, L Lacey; Huang, Huateng; Sukumaran, Jeet; Smith, Stephen A

2018-03-01

Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i.e., discordant loci that indeed reflect incomplete lineage sorting [ILS], as opposed to some other process, such as lateral gene transfer [LGT]), we can analyze this subset using powerful coalescent-based species-tree approaches. Test data sets were simulated where discord among loci could arise from ILS and LGT. Data sets where analyzed using the newly developed program CLASSIPHY (Huang et al., ) to assess whether our ability to distinguish the cause of discord among loci varied when ILS and LGT occurred in the recent versus deep past and whether the accuracy of these inferences were affected by the mutational process. We show that accuracy of probabilistic classification of individual loci by the cause of discord differed when ILS and LGT events occurred more recently compared with the distant past and that the signal-to-noise ratio arising from the mutational process contributes to difficulties in inferring LGT data partitions. We discuss our findings in terms of the promise and limitations of identifying subsets of loci for species-tree inference that will not violate the underlying coalescent model (i.e., data partitions in which ILS, and not LGT, contributes to discord). We also discuss the empirical implications of our work given the many recalcitrant nodes in the tree of life (e.g., origins of angiosperms, amniotes, or Neoaves), and recent arguments for concatenating loci. © 2018 Botanical Society of America.

Traditional and formal ecological knowledge to assess harvesting and conservation of a Mexican Tropical Dry Forest.

PubMed

Monroy-Ortiz, Columba; García-Moya, Edmundo; Romero-Manzanares, Angélica; Luna-Cavazos, Mario; Monroy, Rafael

2018-05-15

This research integrates Traditional and Formal Ecological Knowledge (TEK / FEK) of a Tropical Dry Forest in central Mexico, in order to assess harvesting and conservation of the non-timber forest species. We were interested in: knowing the structure and diversity of the forest community; identifying which are the tree resources of common interest to the users through participatory workshops. A further interest was to identify those resources which are important to local people in terms of preservation; explaining the relationship of the species with some environmental factors; and visualizing which management practices endanger or facilitate the conservation of species. Studied areas were defined and labelled on a map drawn by local informants, where they indicated those plant species of common interest for preservation. Ethnobotanical techniques were used to reveal the TEK and assess harvesting and conservation of the species. With the FEK through community and population ecology, we detected the importance of five environmental factors, obtained various ecological indicators of the vegetation, and studied the population structure of the relevant species. The FEK was analyzed using descriptive and multivariate statistics. As a result, low density and small basal area of trees were registered. Species richness and diversity index were similar to other natural protected areas in Mexico. Tree species harvested shown an asymmetric distribution of diameters. Harvesting, elevation, and accessibility were the most influential factors on tree density. FEK demonstrated that TEK is helpful for the assessment of forest harvesting. Ecological analysis complemented the local knowledge detecting that Lysiloma tergemina is a species non-identified for the people as interesting, although we discover that it is a threatened species by over-harvesting. Haematoxylum brasiletto was identified as important for conservation due to its scarcity and medicinal use. Our results advanced on how the traditional harvesting of tree community has contributed to preserve diversity, when comparing with protected areas. Discrepancies between both kinds of knowledge should be reconciled for contributing to the preservation of priority resources by the local society. Copyright © 2018 Elsevier Ltd. All rights reserved.

How to Identify and Interpret Evolutionary Tree Diagrams

ERIC Educational Resources Information Center

Kong, Yi; Anderson, Trevor; Pelaez, Nancy

2016-01-01

Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly…

Characterization of reference gene expression in tung tree (Vernicia fordii)

USDA-ARS?s Scientific Manuscript database

Tung oil from tung tree (Vernicia fordii) is widely used as a drying ingredient in paints, varnishes, and other coatings and finishes. Recent research has focused on the understanding of the biosynthesis of oil in tung trees. Many oil biosynthetic genes have been identified in tung tree but little...

Minnesota's Forest Trees. Revised.

ERIC Educational Resources Information Center

Miles, William R.; Fuller, Bruce L.

This bulletin describes 46 of the more common trees found in Minnesota's forests and windbreaks. The bulletin contains two tree keys, a summer key and a winter key, to help the reader identify these trees. Besides the two keys, the bulletin includes an introduction, instructions for key use, illustrations of leaf characteristics and twig…

Introduction to Concurrent Engineering: Electronic Circuit Design and Production Applications

DTIC Science & Technology

1992-09-01

STD-1629. Failure mode distribution data for many different types of parts may be found in RAC publication FMD -91. FMEA utilizes inductive logic in a...contrasts with a Fault Tree Analysis ( FTA ) which utilizes deductive logic in a "top down" approach. In FTA , a system failure is assumed and traced down...Analysis ( FTA ) is a graphical method of risk analysis used to identify critical failure modes within a system or equipment. Utilizing a pictorial approach

Data needs for tree removal crash modification factors on Arizona state highways.

DOT National Transportation Integrated Search

2016-07-01

The Arizona Department of Transportation (ADOT) Roadway Departure Safety Implementation Plan (RDSIP) has : identified tree removal as a feasible countermeasure to reduce roadway departure crash frequency or severity. : Previous ADOT work has identifi...

A new method of tree xylem water extraction for isotopic analysis

NASA Astrophysics Data System (ADS)

Gierke, C.; Newton, B. T.

2011-12-01

The Sacramento Mountain Watershed Study in the southern Sacramento Mountains of New Mexico is designed to assess the forest restoration technique of tree thinning in mountain watersheds as an effective method of increasing local and regional groundwater recharge. The project is using a soil water balance approach to quantify the partitioning of local precipitation within this watershed before and after thinning trees. Understanding what sources trees extract their water from (e.g. shallow groundwater, unsaturated fractured bedrock, and soils) is difficult due to a complex hydrologic system and heterogeneous distribution of soil thicknesses. However, in order to accurately quantify the soil water balance and to assess how thinning trees will affect this water balance, it is important determine the sources from which trees extract their water. We plan to use oxygen and hydrogen stable isotopic analysis of various end member waters to identify these different sources. We are in the process of developing a new method of determining the isotopic composition of tree water that has several advantages over conventional methods. Within the tree there is the xylem which transports water from the roots to the leaves and the phloem which transports starches and sugars in a water media throughout the tree. Previous studies have shown that the isotopic composition of xylem water accurately reflects that of source water, while phloem water has undergone isotopic fractionation during photosynthesis and metabolism. The distillation of water from twigs, which is often used to extract tree water for isotopic analysis, is very labor intensive. Other disadvantages to distillation methods include possible fractionation due to phase changes and the possible extraction of fractionated phloem waters. Employing a new mixing method, the composition of the twig water (TW) can be determined by putting twigs of unknown isotopic water composition into waters of known compositions or initial waters (IW), allowing diffusive processes to proceed to equilibrium, measuring the composition of the resulting mixture or final water (FW) then, solving a simple mixing equation. To evaluate this method, we collected several twig samples from Douglas Firs in the Sacramento Mountains. Twig water was prepared for isotopic analysis both by cryogenic distillation and the mixing method. Soil in close proximity to these trees was also sampled and water was extracted by cryogenic distillation. Preliminary results show that the isotopic composition of distilled twig water and soil waters plot to the right of the local meteoric water line (LMWL) suggesting that trees are extracting shallow evaporated soil water. Twig water obtained from the mixing method plot near the LMWL within the range expected for local snow melt, suggesting a possibly deeper non-evaporated source. In general, distillation values are approximately 4% heavier with respect to delta 18O than waters obtained from the mixing method. It is possible that this difference is due to the contribution of the fractionated water of the twig phloem that is released during the distillation process. This difference is quite significant and can lead to very different interpretations. These results are being addressed with additional experiments.

Repeated measures from FIA data facilitates analysis across spatial scales of tree growth responses to nitrogen deposition from individual trees to whole ecoregions

Treesearch

Charles H. (Hobie) Perry; Kevin J. Horn; R. Quinn Thomas; Linda H. Pardo; Erica A.H. Smithwick; Doug Baldwin; Gregory B. Lawrence; Scott W. Bailey; Sabine Braun; Christopher M. Clark; Mark Fenn; Annika Nordin; Jennifer N. Phelan; Paul G. Schaberg; Sam St. Clair; Richard Warby; Shaun Watmough; Steven S. Perakis

2015-01-01

The abundance of temporally and spatially consistent Forest Inventory and Analysis data facilitates hierarchical/multilevel analysis to investigate factors affecting tree growth, scaling from plot-level to continental scales. Herein we use FIA tree and soil inventories in conjunction with various spatial climate and soils data to estimate species-specific responses of...

Identification of Potential Sources of Mercury (Hg) in Farmland Soil Using a Decision Tree Method in China.

PubMed

Zhong, Taiyang; Chen, Dongmei; Zhang, Xiuying

2016-11-09

Identification of the sources of soil mercury (Hg) on the provincial scale is helpful for enacting effective policies to prevent further contamination and take reclamation measurements. The natural and anthropogenic sources and their contributions of Hg in Chinese farmland soil were identified based on a decision tree method. The results showed that the concentrations of Hg in parent materials were most strongly associated with the general spatial distribution pattern of Hg concentration on a provincial scale. The decision tree analysis gained an 89.70% total accuracy in simulating the influence of human activities on the additions of Hg in farmland soil. Human activities-for example, the production of coke, application of fertilizers, discharge of wastewater, discharge of solid waste, and the production of non-ferrous metals-were the main external sources of a large amount of Hg in the farmland soil.

Circum-Arctic petroleum systems identified using decision-tree chemometrics

USGS Publications Warehouse

Peters, K.E.; Ramos, L.S.; Zumberge, J.E.; Valin, Z.C.; Scotese, C.R.; Gautier, D.L.

2007-01-01

Source- and age-related biomarker and isotopic data were measured for more than 1000 crude oil samples from wells and seeps collected above approximately 55??N latitude. A unique, multitiered chemometric (multivariate statistical) decision tree was created that allowed automated classification of 31 genetically distinct circumArctic oil families based on a training set of 622 oil samples. The method, which we call decision-tree chemometrics, uses principal components analysis and multiple tiers of K-nearest neighbor and SIMCA (soft independent modeling of class analogy) models to classify and assign confidence limits for newly acquired oil samples and source rock extracts. Geochemical data for each oil sample were also used to infer the age, lithology, organic matter input, depositional environment, and identity of its source rock. These results demonstrate the value of large petroleum databases where all samples were analyzed using the same procedures and instrumentation. Copyright ?? 2007. The American Association of Petroleum Geologists. All rights reserved.

Identification of Potential Sources of Mercury (Hg) in Farmland Soil Using a Decision Tree Method in China

PubMed Central

Zhong, Taiyang; Chen, Dongmei; Zhang, Xiuying

2016-01-01

Identification of the sources of soil mercury (Hg) on the provincial scale is helpful for enacting effective policies to prevent further contamination and take reclamation measurements. The natural and anthropogenic sources and their contributions of Hg in Chinese farmland soil were identified based on a decision tree method. The results showed that the concentrations of Hg in parent materials were most strongly associated with the general spatial distribution pattern of Hg concentration on a provincial scale. The decision tree analysis gained an 89.70% total accuracy in simulating the influence of human activities on the additions of Hg in farmland soil. Human activities—for example, the production of coke, application of fertilizers, discharge of wastewater, discharge of solid waste, and the production of non-ferrous metals—were the main external sources of a large amount of Hg in the farmland soil. PMID:27834884

Vegetation optical depth measured by microwave radiometry as an indicator of tree mortality risk

NASA Astrophysics Data System (ADS)

Rao, K.; Anderegg, W.; Sala, A.; Martínez-Vilalta, J.; Konings, A. G.

2017-12-01

Increased drought-related tree mortality has been observed across several regions in recent years. Vast spatial extent and high temporal variability makes field monitoring of tree mortality cumbersome and expensive. With global coverage and high temporal revisit, satellite remote sensing offers an unprecedented tool to monitor terrestrial ecosystems and identify areas at risk of large drought-driven tree mortality events. To date, studies that use remote sensing data to monitor tree mortality have focused on external climatic thresholds such as temperature and evapotranspiration. However, this approach fails to consider internal water stress in vegetation - which can vary across trees even for similar climatic conditions due to differences in hydraulic behavior, soil type, etc - and may therefore be a poor basis for measuring mortality events. There is a consensus that xylem hydraulic failure often precedes drought-induced mortality, suggesting depleted canopy water content shortly before onset of mortality. Observations of vegetation optical depth (VOD) derived from passive microwave are proportional to canopy water content. In this study, we propose to use variations in VOD as an indicator of potential tree mortality. Since VOD accounts for intrinsic water stress undergone by vegetation, it is expected to be more accurate than external climatic stress indicators. Analysis of tree mortality events in California, USA observed by airborne detection shows a consistent relationship between mortality and the proposed VOD metric. Although this approach is limited by the kilometer-scale resolution of passive microwave radiometry, our results nevertheless demonstrate that microwave-derived estimates of vegetation water content can be used to study drought-driven tree mortality, and may be a valuable tool for mortality predictions if they can be combined with higher-resolution variables.

Isolation and identification of symbiotic bacteria from the skin, mouth, and rectum of wild and captive tree shrews.

PubMed

Li, Gui; Lai, Ren; Duan, Gang; Lyu, Long-Bao; Zhang, Zhi-Ye; Liu, Huang; Xiang, Xun

2014-11-18

Endosymbionts influence many aspects of their hosts' health conditions, including physiology, development, immunity, metabolism, etc. Tree shrews (Tupaia belangeri chinensis) have attracted increasing attention in modeling human diseases and therapeutic responses due to their close relationship with primates. To clarify the situation of symbiotic bacteria from their body surface, oral cavity, and anus, 12 wild and 12 the third generation of captive tree shrews were examined. Based on morphological and cultural characteristics, physiological and biochemical tests, as well as the 16S rDNA full sequence analysis, 12 bacteria strains were isolated and identified from the wild tree shrews: body surface: Bacillus subtilis (detection rate 42%), Pseudomonas aeruginosa (25%), Staphlococcus aureus (33%), S. Epidermidis (75%), Micrococcus luteus (25%), Kurthia gibsonii (17%); oral cavity: Neisseria mucosa (58%), Streptococcus pneumonia (17%); anus: Enterococcus faecalis (17%), Lactococus lactis (33%), Escherichia coli (92%), Salmonella typhosa (17%); whereas, four were indentified from the third generation captive tree shrews: body surface: S. epidermidis (75%); oral cavity: N.mucosa (67%); anus: L. lactis (33%), E. coli (100%). These results indicate that S. epidermidis, N. mucosa, L. lactis and E. coli were major bacteria in tree shrews, whereas, S. aureus, M. luteus, K. gibsonii, E. faecalis and S. typhosa were species-specific flora. This study facilitates the future use of tree shrews as a standard experimental animal and improves our understanding of the relationship between endosymbionts and their hosts.

Risk assessment for enterprise resource planning (ERP) system implementations: a fault tree analysis approach

NASA Astrophysics Data System (ADS)

Zeng, Yajun; Skibniewski, Miroslaw J.

2013-08-01

Enterprise resource planning (ERP) system implementations are often characterised with large capital outlay, long implementation duration, and high risk of failure. In order to avoid ERP implementation failure and realise the benefits of the system, sound risk management is the key. This paper proposes a probabilistic risk assessment approach for ERP system implementation projects based on fault tree analysis, which models the relationship between ERP system components and specific risk factors. Unlike traditional risk management approaches that have been mostly focused on meeting project budget and schedule objectives, the proposed approach intends to address the risks that may cause ERP system usage failure. The approach can be used to identify the root causes of ERP system implementation usage failure and quantify the impact of critical component failures or critical risk events in the implementation process.

Identifying the critical success factors in the coverage of low vision services using the classification analysis and regression tree methodology.

PubMed

Chiang, Peggy Pei-Chia; Xie, Jing; Keeffe, Jill Elizabeth

2011-04-25

To identify the critical success factors (CSF) associated with coverage of low vision services. Data were collected from a survey distributed to Vision 2020 contacts, government, and non-government organizations (NGOs) in 195 countries. The Classification and Regression Tree Analysis (CART) was used to identify the critical success factors of low vision service coverage. Independent variables were sourced from the survey: policies, epidemiology, provision of services, equipment and infrastructure, barriers to services, human resources, and monitoring and evaluation. Socioeconomic and demographic independent variables: health expenditure, population statistics, development status, and human resources in general, were sourced from the World Health Organization (WHO), World Bank, and the United Nations (UN). The findings identified that having >50% of children obtaining devices when prescribed (χ(2) = 44; P < 0.000), multidisciplinary care (χ(2) = 14.54; P = 0.002), >3 rehabilitation workers per 10 million of population (χ(2) = 4.50; P = 0.034), higher percentage of population urbanized (χ(2) = 14.54; P = 0.002), a level of private investment (χ(2) = 14.55; P = 0.015), and being fully funded by government (χ(2) = 6.02; P = 0.014), are critical success factors associated with coverage of low vision services. This study identified the most important predictors for countries with better low vision coverage. The CART is a useful and suitable methodology in survey research and is a novel way to simplify a complex global public health issue in eye care.

Enhanced visualization of the retinal vasculature using depth information in OCT.

PubMed

de Moura, Joaquim; Novo, Jorge; Charlón, Pablo; Barreira, Noelia; Ortega, Marcos

2017-12-01

Retinal vessel tree extraction is a crucial step for analyzing the microcirculation, a frequently needed process in the study of relevant diseases. To date, this has normally been done by using 2D image capture paradigms, offering a restricted visualization of the real layout of the retinal vasculature. In this work, we propose a new approach that automatically segments and reconstructs the 3D retinal vessel tree by combining near-infrared reflectance retinography information with Optical Coherence Tomography (OCT) sections. Our proposal identifies the vessels, estimates their calibers, and obtains the depth at all the positions of the entire vessel tree, thereby enabling the reconstruction of the 3D layout of the complete arteriovenous tree for subsequent analysis. The method was tested using 991 OCT images combined with their corresponding near-infrared reflectance retinography. The different stages of the methodology were validated using the opinion of an expert as a reference. The tests offered accurate results, showing coherent reconstructions of the 3D vasculature that can be analyzed in the diagnosis of relevant diseases affecting the retinal microcirculation, such as hypertension or diabetes, among others.

Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang

2012-12-28

Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp.more » variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks.« less

Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

PubMed Central

Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang; Lao, Jeemeng; George, Anthe; Hong, Kunlun; Henry, Robert; Simmons, Blake A.; Heazlewood, Joshua L.; Holmes, Bradley M.

2012-01-01

Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks. PMID:23300786

Super High Resolution Airborne Remote Sensing for Evaluating the Decomposition Function of Ecosystem of Temperate Forest in Japan

NASA Astrophysics Data System (ADS)

Suzuki, R.; Fadaei, H.; Ishii, R.; Nagai, S.; Okabe, K.; Yamashita, S.; Taki, H.; Honda, Y.; Kajiwara, K.

2013-12-01

Forest ecosystem is sustained by nutrients cycle among trees, floor vegetation, litter, and soil etc. One of important driving mechanisms for such nutrients cycle is the decomposition of the fallen trees by fungi, and this process would play an important function in the biogeochemical cycle of the environment. This study challenged to identify the position and size of fallen trees in a temperate forest in Japan based on super high resolution (less than 1cm) visual images taken from a camera aboard a helicopter. Field campaign was carried out on November 29, 2011 at the experimental forest (6 ha, 300m x 200m, 36° 56' 10.5'N, 140° 35' 16.5'E) in Kitaibaraki, Ibaraki, Japan. According to the census survey of the forest, deciduous broad leave trees are dominant. There was almost no leaf in the forest crown on the day of the field campaign, and that brought a high visibility of the floor from the sky. The topography of the forest site is characterized by a small valley with a river flowing north to south at its bottom. An unmanned helicopter (Yamaha RMAX G1) flew over the forest in north-south lines with a speed of 3m/s at height of 30-70m from the ground surface. The interval between adjacent two lines was 20m. A consumer grade camera (Canon EOS Kiss X5 with 55mm lens; 5184 x 3456 pixels) was fixed with the vertically looking down direction on the helicopter. The camera took forest images with 5 seconds interval. The helicopter was also equipped by a laser range finder (LRF) (SkEyesBOX MP-1). Based on the point cloud created by the LRF measurement, 1 x 1m digital elevation model (DEM) of the ground surface was established by finding the lowest point value of the point cloud in each 1 x 1m grid of the forest. The forest was covered by 211 images taken by the camera. Each image was orthorectified by using the DEM and the data of the position and orientations of the helicopter, and then they were mosaicked into one image. Fallen trees with the diameter more than 10cm were targeted for the analysis, and we confirmed that some of fallen tree was easily to identify visually, but some of them was hard to identify because the branch and trunk of trees hided fallen trees. We are going develop the automatic detection algorithm by decision tree and object-based classifications, and then validate the algorithm with in situ information.

Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area.

PubMed

Greenwood, Sarah; Ruiz-Benito, Paloma; Martínez-Vilalta, Jordi; Lloret, Francisco; Kitzberger, Thomas; Allen, Craig D; Fensham, Rod; Laughlin, Daniel C; Kattge, Jens; Bönisch, Gerhard; Kraft, Nathan J B; Jump, Alistair S

2017-04-01

Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees -1  year -1 ) increased 0.46 (95% CI = 0.2-0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future. © 2017 John Wiley & Sons Ltd/CNRS.

Reference Canopy Stomatal Conductance Explains Spatiotemporal Patterns of Tree Transpiration

NASA Astrophysics Data System (ADS)

Loranty, M. M.; Mackay, D. S.; Ewers, B. E.; Kruger, E. L.; Traver, E.

2007-12-01

Increased heterogeneity in patterns of whole tree transpiration (EC) with increasing atmospheric vapor pressure deficit (D) suggests a dynamic response of sap flow velocity (JS) to environmental drivers. We hypothesized that differences in reference stomatal conductance (GSref), stomatal conductance at D = 1kPa, would explain the spatiotemporal dynamics of JS. Using a coupled model of plant hydraulic and biochemical processes we tested this hypothesis with sap flux data for 106 aspen ( Populus tremuloides) and 108 sugar maple ( Acer saccharum) trees collected from plots using in 2-D cyclic sampling scheme during the summer of 2005 in northern Wisconsin. Inverse modeling is used to estimate GSref for each tree. For each species, trees from across the ranges of JS and diameter distributions are compared. GSref explained temporal variability in spatial patterns of EC We explore several possible mechanistic explanations for differences in GSref among trees. Topoedaphic factors are considered to determine if location within a stand has an effect. We also consider competition with neighboring individuals as a possible explanation. Variations in GSref in aspen were explained in part by competition for light between neighboring individuals, while competition for light was not a significant factor for sugar maple. Based on simulation analysis we identify possible biochemical feedbacks as drivers of the variability in plant hydraulics. Other factors examined included micro-topography within both sites.

Chemical hazards database and detection system for Microgravity and Materials Processing Facility (MMPF)

NASA Technical Reports Server (NTRS)

Steele, Jimmy; Smith, Robert E.

1991-01-01

The ability to identify contaminants associated with experiments and facilities is directly related to the safety of the Space Station. A means of identifying these contaminants has been developed through this contracting effort. The delivered system provides a listing of the materials and/or chemicals associated with each facility, information as to the contaminant's physical state, a list of the quantity and/or volume of each suspected contaminant, a database of the toxicological hazards associated with each contaminant, a recommended means of rapid identification of the contaminants under operational conditions, a method of identifying possible failure modes and effects analysis associated with each facility, and a fault tree-type analysis that will provide a means of identifying potential hazardous conditions related to future planned missions.

Biophysical modelling of intra-ring variations in tracheid features and wood density of Pinus pinaster trees exposed to seasonal droughts.

PubMed

Wilkinson, Sarah; Ogée, Jérôme; Domec, Jean-Christophe; Rayment, Mark; Wingate, Lisa

2015-03-01

Process-based models that link seasonally varying environmental signals to morphological features within tree rings are essential tools to predict tree growth response and commercially important wood quality traits under future climate scenarios. This study evaluated model portrayal of radial growth and wood anatomy observations within a mature maritime pine (Pinus pinaster (L.) Aït.) stand exposed to seasonal droughts. Intra-annual variations in tracheid anatomy and wood density were identified through image analysis and X-ray densitometry on stem cores covering the growth period 1999-2010. A cambial growth model was integrated with modelled plant water status and sugar availability from the soil-plant-atmosphere transfer model MuSICA to generate estimates of cell number, cell volume, cell mass and wood density on a weekly time step. The model successfully predicted inter-annual variations in cell number, ring width and maximum wood density. The model was also able to predict the occurrence of special anatomical features such as intra-annual density fluctuations (IADFs) in growth rings. Since cell wall thickness remained surprisingly constant within and between growth rings, variations in wood density were primarily the result of variations in lumen diameter, both in the model and anatomical data. In the model, changes in plant water status were identified as the main driver of the IADFs through a direct effect on cell volume. The anatomy data also revealed that a trade-off existed between hydraulic safety and hydraulic efficiency. Although a simplified description of cambial physiology is presented, this integrated modelling approach shows potential value for identifying universal patterns of tree-ring growth and anatomical features over a broad climatic gradient. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae).

PubMed

Failla, A J; Vasquez, A A; Hudson, P; Fujimoto, M; Ram, J L

2016-02-01

Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassessment of chironomid communities.

Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae)

USGS Publications Warehouse

Failla, Andrew Joseph; Vasquez, Adrian Amelio; Hudson, Patrick L.; Fujimoto, Masanori; Ram, Jeffrey L.

2016-01-01

Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or ‘species group’ level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassesment of chironomid communities.

Genome-wide identification of WRKY family genes in peach and analysis of WRKY expression during bud dormancy.

PubMed

Chen, Min; Tan, Qiuping; Sun, Mingyue; Li, Dongmei; Fu, Xiling; Chen, Xiude; Xiao, Wei; Li, Ling; Gao, Dongsheng

2016-06-01

Bud dormancy in deciduous fruit trees is an important adaptive mechanism for their survival in cold climates. The WRKY genes participate in several developmental and physiological processes, including dormancy. However, the dormancy mechanisms of WRKY genes have not been studied in detail. We conducted a genome-wide analysis and identified 58 WRKY genes in peach. These putative genes were located on all eight chromosomes. In bioinformatics analyses, we compared the sequences of WRKY genes from peach, rice, and Arabidopsis. In a cluster analysis, the gene sequences formed three groups, of which group II was further divided into five subgroups. Gene structure was highly conserved within each group, especially in groups IId and III. Gene expression analyses by qRT-PCR showed that WRKY genes showed different expression patterns in peach buds during dormancy. The mean expression levels of six WRKY genes (Prupe.6G286000, Prupe.1G393000, Prupe.1G114800, Prupe.1G071400, Prupe.2G185100, and Prupe.2G307400) increased during endodormancy and decreased during ecodormancy, indicating that these six WRKY genes may play a role in dormancy in a perennial fruit tree. This information will be useful for selecting fruit trees with desirable dormancy characteristics or for manipulating dormancy in genetic engineering programs.

Mapping urban forest tree species using IKONOS imagery: preliminary results.

PubMed

Pu, Ruiliang

2011-01-01

A stepwise masking system with high-resolution IKONOS imagery was developed to identify and map urban forest tree species/groups in the City of Tampa, Florida, USA. The eight species/groups consist of sand live oak (Quercus geminata), laurel oak (Quercus laurifolia), live oak (Quercus virginiana), magnolia (Magnolia grandiflora), pine (species group), palm (species group), camphor (Cinnamomum camphora), and red maple (Acer rubrum). The system was implemented with soil-adjusted vegetation index (SAVI) threshold, textural information after running a low-pass filter, and brightness threshold of NIR band to separate tree canopies from non-vegetated areas from other vegetation types (e.g., grass/lawn) and to separate the tree canopies into sunlit and shadow areas. A maximum likelihood classifier was used to identify and map forest type and species. After IKONOS imagery was preprocessed, a total of nine spectral features were generated, including four spectral bands, three hue-intensity-saturation indices, one SAVI, and one texture image. The identified and mapped results were examined with independent ground survey data. The experimental results indicate that when classifying all the eight tree species/ groups with the high-resolution IKONOS image data, the identifying accuracy was very low and could not satisfy a practical application level, and when merging the eight species/groups into four major species/groups, the average accuracy is still low (average accuracy = 73%, overall accuracy = 86%, and κ = 0.76 with sunlit test samples). Such a low accuracy of identifying and mapping the urban tree species/groups is attributable to low spatial resolution IKONOS image data relative to tree crown size, to complex and variable background spectrum impact on crown spectra, and to shadow/shaded impact. The preliminary results imply that to improve the tree species identification accuracy and achieve a practical application level in urban area, multi-temporal (multi-seasonal) or hyperspectral data image data should be considered for use in the future.

Community trees: Identifying codiversification in the Páramo dipteran community.

PubMed

Carstens, Bryan C; Gruenstaeudl, Michael; Reid, Noah M

2016-05-01

Groups of codistributed species that responded in a concerted manner to environmental events are expected to share patterns of evolutionary diversification. However, the identification of such groups has largely been based on qualitative, post hoc analyses. We develop here two methods (posterior predictive simulation [PPS], Kuhner-Felsenstein [K-F] analysis of variance [ANOVA]) for the analysis of codistributed species that, given a group of species with a shared pattern of diversification, allow empiricists to identify those taxa that do not codiversify (i.e., "outlier" species). The identification of outlier species makes it possible to jointly estimate the evolutionary history of co-diversifying taxa. To evaluate the approaches presented here, we collected data from Páramo dipterans, identified outlier species, and estimated a "community tree" from species that are identified as having codiversified. Our results demonstrate that dipteran communities from different Páramo habitats in the same mountain range are more closely related than communities in other ranges. We also conduct simulation testing to evaluate this approach. Results suggest that our approach provides a useful addition to comparative phylogeographic methods, while identifying aspects of the analysis that require careful interpretation. In particular, both the PPS and K-F ANOVA perform acceptably when there are one or two outlier species, but less so as the number of outliers increases. This is likely a function of the corresponding degradation of the signal of community divergence; without a strong signal from a codiversifying community, there is no dominant pattern from which to detect an outlier species. For this reason, both the magnitude of K-F distance distribution and outside knowledge about the phylogeographic history of each putative member of the community should be considered when interpreting the results. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Hierarchical structures of correlations networks among Turkey’s exports and imports by currencies

NASA Astrophysics Data System (ADS)

Kocakaplan, Yusuf; Deviren, Bayram; Keskin, Mustafa

2012-12-01

We have examined the hierarchical structures of correlations networks among Turkey’s exports and imports by currencies for the 1996-2010 periods, using the concept of a minimal spanning tree (MST) and hierarchical tree (HT) which depend on the concept of ultrametricity. These trees are useful tools for understanding and detecting the global structure, taxonomy and hierarchy in financial markets. We derived a hierarchical organization and build the MSTs and HTs during the 1996-2001 and 2002-2010 periods. The reason for studying two different sub-periods, namely 1996-2001 and 2002-2010, is that the Euro (EUR) came into use in 2001, and some countries have made their exports and imports with Turkey via the EUR since 2002, and in order to test various time-windows and observe temporal evolution. We have carried out bootstrap analysis to associate a value of the statistical reliability to the links of the MSTs and HTs. We have also used the average linkage cluster analysis (ALCA) to observe the cluster structure more clearly. Moreover, we have obtained the bidimensional minimal spanning tree (BMST) due to economic trade being a bidimensional problem. From the structural topologies of these trees, we have identified different clusters of currencies according to their proximity and economic ties. Our results show that some currencies are more important within the network, due to a tighter connection with other currencies. We have also found that the obtained currencies play a key role for Turkey’s exports and imports and have important implications for the design of portfolio and investment strategies.

Evaluation of the genetic diversity of Plum pox virus in a single plum tree.

PubMed

Predajňa, Lukáš; Šubr, Zdeno; Candresse, Thierry; Glasa, Miroslav

2012-07-01

Genetic diversity of Plum pox virus (PPV) and its distribution within a single perennial woody host (plum, Prunus domestica) has been evaluated. A plum tree was triply infected by chip-budding with PPV-M, PPV-D and PPV-Rec isolates in 2003 and left to develop untreated under open field conditions. In September 2010 leaf and fruit samples were collected from different parts of the tree canopy. A 745-bp NIb-CP fragment of PPV genome, containing the hypervariable region encoding the CP N-terminal end was amplified by RT-PCR from each sample and directly sequenced to determine the dominant sequence. In parallel, the PCR products were cloned and a total of 105 individual clones were sequenced. Sequence analysis revealed that after 7 years of infection, only PPV-M was still detectable in the tree and that the two other isolates (PPV-Rec and PPV-D) had been displaced. Despite the fact that the analysis targeted a relatively short portion of the genome, a substantial amount of intra-isolate variability was observed for PPV-M. A total of 51 different haplotypes could be identified from the 105 individual sequences, two of which were largely dominant. However, no clear-cut structuration of the viral population by the tree architecture could be highlighted although the results obtained suggest the possibility of intra-leaf/fruit differentiation of the viral population. Comparison of the consensus sequence with the original source isolate showed no difference, suggesting within-plant stability of this original isolate under open field conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

Use hyperspectral remote sensing technique to monitoring pine wood nomatode disease preliminary

NASA Astrophysics Data System (ADS)

Qin, Lin; Wang, Xianghong; Jiang, Jing; Yang, Xianchang; Ke, Daiyan; Li, Hongqun; Wang, Dingyi

2016-10-01

The pine wilt disease is a devastating disease of pine trees. In China, the first discoveries of the pine wilt disease on 1982 at Dr. Sun Yat-sen's Mausoleum in Nanjing. It occurred an area of 77000 hm2 in 2005, More than 1540000 pine trees deaths in the year. Many districts of Chongqing in Three Gorges Reservoir have different degrees of pine wilt disease occurrence. It is a serious threat to the ecological environment of the reservoir area. Use unmanned airship to carry high spectrum remote sensing monitoring technology to develop the study on pine wood nematode disease early diagnosis and early warning and forecasting in this study. The hyper spectral data and the digital orthophoto map data of Fuling District Yongsheng Forestry had been achieved In September 2015. Using digital image processing technology to deal with the digital orthophoto map, the number of disease tree and its distribution is automatic identified. Hyper spectral remote sensing data is processed by the spectrum comparison algorithm, and the number and distribution of disease pine trees are also obtained. Two results are compared, the distribution area of disease pine trees are basically the same, indicating that using low air remote sensing technology to monitor the pine wood nematode distribution is successful. From the results we can see that the hyper spectral data analysis results more accurate and less affected by environmental factors than digital orthophoto map analysis results, and more environment variable can be extracted, so the hyper spectral data study is future development direction.

An overview of the phase-modular fault tree approach to phased mission system analysis

NASA Technical Reports Server (NTRS)

Meshkat, L.; Xing, L.; Donohue, S. K.; Ou, Y.

2003-01-01

We look at how fault tree analysis (FTA), a primary means of performing reliability analysis of PMS, can meet this challenge in this paper by presenting an overview of the modular approach to solving fault trees that represent PMS.

Expressed sequence tag (EST) analysis of the pine wood nematode Bursaphelenchus xylophilus and B. mucronatus.

PubMed

Kikuchi, Taisei; Aikawa, Takuya; Kosaka, Hajime; Pritchard, Leighton; Ogura, Nobuo; Jones, John T

2007-09-01

Most Bursaphelenchus species feed on fungi that colonise dead or dying trees. However, Bursaphelenchus xylophilus is unique in that in addition to feeding on fungi it has the capacity to be a parasite of live pine trees. We present an analysis of over 13,000 expressed sequence tags (ESTs) from B. xylophilus and, by way of contrast, over 3000 ESTs from a closely related species that does not parasitise plants as readily; B. mucronatus. Four libraries from B. xylophilus, from a variety of life stages including fungal feeding nematodes, nematodes extracted from plants and dauer-like stage nematodes, and one library from B. mucronatus were constructed and used to generate ESTs. Contig analysis showed that the 13,327 B. xylophilus ESTs could be grouped into 2110 contigs and 4377 singletons giving a total of 6487 identified genes. Similarly the 3193 B. mucronatus ESTs yielded a total of 2219 identified genes from 425 contigs and 1794 singletons. A variety of proteins potentially important in the parasitic process of B. xylophilus and B. mucronatus, including plant and fungal cell wall degrading enzymes and a novel gene potentially encoding a expansin-like protein that may disrupt non-covalent bonds in the plant cell wall were identified in the libraries. Additionally several gene candidates potentially involved in dauer entry or maintenance were also identified in the EST dataset. The EST sequences from this study will provide a solid base for future research on the biology, pathogenicity and evolutionary history of this nematode group.

Automated method for the identification and analysis of vascular tree structures in retinal vessel network

NASA Astrophysics Data System (ADS)

Joshi, Vinayak S.; Garvin, Mona K.; Reinhardt, Joseph M.; Abramoff, Michael D.

2011-03-01

Structural analysis of retinal vessel network has so far served in the diagnosis of retinopathies and systemic diseases. The retinopathies are known to affect the morphologic properties of retinal vessels such as course, shape, caliber, and tortuosity. Whether the arteries and the veins respond to these changes together or in tandem has always been a topic of discussion. However the diseases such as diabetic retinopathy and retinopathy of prematurity have been diagnosed with the morphologic changes specific either to arteries or to veins. Thus a method describing the separation of retinal vessel trees imaged in a two dimensional color fundus image may assist in artery-vein classification and quantitative assessment of morphologic changes particular to arteries or veins. We propose a method based on mathematical morphology and graph search to identify and label the retinal vessel trees, which provides a structural mapping of vessel network in terms of each individual primary vessel, its branches and spatial positions of branching and cross-over points. The method was evaluated on a dataset of 15 fundus images resulting into an accuracy of 92.87 % correctly assigned vessel pixels when compared with the manual labeling of separated vessel trees. Accordingly, the structural mapping method performs well and we are currently investigating its potential in evaluating the characteristic properties specific to arteries or veins.

Multicriteria evaluation of simulated logging scenarios in a tropical rain forest.

PubMed

Huth, Andreas; Drechsler, Martin; Köhler, Peter

2004-07-01

Forest growth models are useful tools for investigating the long-term impacts of logging. In this paper, the results of the rain forest growth model FORMIND were assessed by a multicriteria decision analysis. The main processes covered by FORMIND include tree growth, mortality, regeneration and competition. Tree growth is calculated based on a carbon balance approach. Trees compete for light and space; dying large trees fall down and create gaps in the forest. Sixty-four different logging scenarios for an initially undisturbed forest stand at Deramakot (Malaysia) were simulated. The scenarios differ regarding the logging cycle, logging method, cutting limit and logging intensity. We characterise the impacts with four criteria describing the yield, canopy opening and changes in species composition. Multicriteria decision analysis was used for the first time to evaluate the scenarios and identify the efficient ones. Our results plainly show that reduced-impact logging scenarios are more 'efficient' than the others, since in these scenarios forest damage is minimised without significantly reducing yield. Nevertheless, there is a trade-off between yield and achieving a desired ecological state of logged forest; the ecological state of the logged forests can only be improved by reducing yields and enlarging the logging cycles. Our study also demonstrates that high cutting limits or low logging intensities cannot compensate for the high level of damage caused by conventional logging techniques.

Mapping Forest Structure From Tree Clump And Opening Patterns Across Landscapes With Airborne Lidar To Study Response To Disturbances And Map Habitat

NASA Astrophysics Data System (ADS)

Kane, V. R.; McGaughey, R. J.; Asner, G. P.; Kane, J. T.; Churchill, D.; Vaughn, N.

2016-12-01

Most natural forests are structured as mosaics of tree clumps and openings. These mosaics reflect both the underlying patterns of the biophysical environment and the finer scale patterns of disturbance and regrowth. We have developed methods to quantify and map patterns of tree clumps and openings at scales from within stands to landscapes using airborne LiDAR. While many studies have used LiDAR data to identify individual trees, we also identify clumps as adjacent trees with similar heights within a stand that likely established at a similar time following a disturbance. We characterize openings by both size class and shape complexity. Spatial statistics are used to identify patterns of tree clumps and openings at the local (0.81 ha) scale, and these patterns are then mapped across entire landscapes. We use LiDAR data acquired over Sequoia National Park, California, USA, to show how forest structure varies with patterns of productivity driven by the biophysical environment. We then show how clump and opening patterns vary with different fire histories and how recent drought mortality correlates with different tree clump and opening structural mosaics. We also demonstrate that nesting sites for the California spotted owl, a species of concern, are associated with clumps of large (>32 and especially >48 m) trees but that the surrounding foraging areas consist of a heterogeneous pattern of forest structure. These methods are especially useful for studying clumps of large trees, which dominate above ground forest biomass, and the effects of disturbance on the abundance and pattern of large trees as key forest structures.

NVivo 8 and consistency in data analysis: reflecting on the use of a qualitative data analysis program.

PubMed

Bergin, Michael

2011-01-01

Qualitative data analysis is a complex process and demands clear thinking on the part of the analyst. However, a number of deficiencies may obstruct the research analyst during the process, leading to inconsistencies occurring. This paper is a reflection on the use of a qualitative data analysis program, NVivo 8, and its usefulness in identifying consistency and inconsistency during the coding process. The author was conducting a large-scale study of providers and users of mental health services in Ireland. He used NVivo 8 to store, code and analyse the data and this paper reflects some of his observations during the study. The demands placed on the analyst in trying to balance the mechanics of working through a qualitative data analysis program, while simultaneously remaining conscious of the value of all sources are highlighted. NVivo 8 as a qualitative data analysis program is a challenging but valuable means for advancing the robustness of qualitative research. Pitfalls can be avoided during analysis by running queries as the analyst progresses from tree node to tree node rather than leaving it to a stage whereby data analysis is well advanced.

Who Died, Where? Quantification of Drought-Induced Tree Mortality in Texas

NASA Astrophysics Data System (ADS)

Schwantes, A.; Swenson, J. J.; Johnson, D. M.; Domec, J. C.; Jackson, R. B.

2014-12-01

During 2011, Texas experienced a severe drought that killed millions of trees across the state. Drought-induced tree mortality can have significant ecological impacts and is expected to increase with climate change. We identify methods to quantify tree mortality in central Texas by using remotely sensed images before and after the drought at multiple spatial resolutions. Fine-scale tree mortality maps were created by classifying 1-m orthophotos from the National Agriculture Imagery Program. These classifications showed a high correlation with field estimates of percent canopy loss (RMSE = 2%; R2=0.9), and were thus used to calibrate coarser scale 30-m Landsat imagery. Random Forest, a machine learning method, was applied to obtain sub-pixel estimates of tree mortality. Traditional per-pixel classification techniques can map mortality of whole stands of trees (e.g. fire). However, these methods are often inadequate in detecting subtle changes in land cover, such as those associated with drought-induced tree mortality, which is often a widespread but scattered disturbance. Our method is unique, because it is capable of mapping death of individual canopies within a pixel. These 30-m tree mortality maps were then used to identify ecological systems most impacted by the drought and edaphic factors that control spatial distributions of tree mortality across central Texas. Ground observations coupled with our remote sensing analyses revealed that the majority of the mortality was Juniperus ashei. From a physiological standpoint this is surprising, because J. ashei is a drought-resistant tree. However, over the last century, this species has recently encroached into many areas previously dominated by grassland. Also, J. ashei tends to occupy landscape positions with lower available water storage, which could explain its high mortality rate. Predominantly tree mortality occurred in dry landscape positions (e.g. areas dominated by shallow soils, a low compound topographic index, and a high heat index). As increases in extreme drought events are predicted to occur with climate change, it will become more important to establish methods capable of detecting associated drought-induced tree mortality, to recognize vulnerable ecological systems, and to identify edaphic factors that predispose trees to mortality.

Classification tree analysis to enhance targeting for follow-up exam of colorectal cancer screening

PubMed Central

2013-01-01

Background Follow-up rate after a fecal occult blood test (FOBT) is low worldwide. In order to increase the follow-up rate, segmentation of the target population has been proposed as a promising strategy, because an intervention can then be tailored toward specific subgroups of the population rather than using one type of intervention for all groups. The aim of this study is to identify subgroups that share the same patterns of characteristics related to follow-up exams after FOBT. Methods The study sample consisted of 143 patients aged 50–69 years who were requested to undergo follow-up exams after FOBT. A classification tree analysis was performed, using the follow-up rate as a dependent variable and sociodemographic variables, psychological variables, past FOBT and follow-up exam, family history of colorectal cancer (CRC), and history of bowel disease as predictive variables. Results The follow-up rate in 143 participants was 74.1% (n = 106). A classification tree analysis identified four subgroups as follows; (1) subgroup with a high degree of fear of CRC, unemployed and with a history of bowel disease (n = 24, 100.0% follow-up rate), (2) subgroup with a high degree of fear of CRC, unemployed and with no history of bowel disease (n = 17, 82.4% follow-up rate), (3) subgroup with a high degree of fear of CRC and employed (n = 24, 66.7% follow-up rate), and (4) subgroup with a low degree of fear of CRC (n = 78, 66.7% follow-up rate). Conclusion The identification of four subgroups with a diverse range of follow-up rates for CRC screening indicates the direction to take in future development of an effective tailored intervention strategy. PMID:24112563

Enhancing the Possibility of Success by Measuring the Probability of Failure in an Educational Program.

ERIC Educational Resources Information Center

Brookhart, Susan M.; And Others

1997-01-01

Process Analysis is described as a method for identifying and measuring the probability of events that could cause the failure of a program, resulting in a cause-and-effect tree structure of events. The method is illustrated through the evaluation of a pilot instructional program at an elementary school. (SLD)

Knowledge and Community: The Effect of a First-Year Seminar on Student Persistence

ERIC Educational Resources Information Center

Pittendrigh, Adele; Borkowski, John; Swinford, Steven; Plumb, Carolyn

2016-01-01

This study explores the effects of an academic seminar on the persistence of first-year college students, including effects on students most at risk of dropping out. A secondary interest was demonstrating the utility of using classification and regression tree analysis to identify relevant predictors of student persistence. The results of the…

HPLC-MS analysis of secondary metabolites in leaves from orange trees infected with Huanglongbing: A 9-month time series study

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB) disease, presumably caused by Canditatus Liberibacter asiaticus (CLas), is threatening one million acres of commercial citrus groves that have an annual production value of approximately $3 billion across the U.S. The objectives of this study were to identify the earliest signifi...

Model Choice and Sample Size in Item Response Theory Analysis of Aphasia Tests

ERIC Educational Resources Information Center

Hula, William D.; Fergadiotis, Gerasimos; Martin, Nadine

2012-01-01

Purpose: The purpose of this study was to identify the most appropriate item response theory (IRT) measurement model for aphasia tests requiring 2-choice responses and to determine whether small samples are adequate for estimating such models. Method: Pyramids and Palm Trees (Howard & Patterson, 1992) test data that had been collected from…

A Multi-stakeholder Approach to Moving Beyond Tree Mortality in the Sierra Nevada

NASA Astrophysics Data System (ADS)

Balachowski, J.; Buluc, L.; Fischer, C.; Ko, J.; Ostoja, S.

2017-12-01

The US Forest Service has estimated that 102 million trees have died in California since 2010. This die off event has been attributed to the combined effects of historical land management practices, fire suppression, insect outbreaks, and climate-related stressors. This tree mortality event represents the largest and most significant ecological disturbance in California in centuries, if not longer. Both scientists and managers recognize the need to rethink our approach to forest management in the face of a changing climate and increasingly frequent, uncharacteristically large wildfires, while budgets and staffing capacity continue to decrease. Addressing the uncertainly in managing under climate change with fewer financial resources will require multiple partners and stakeholders—including federal and state agencies, local governments, and non-governmental organizations—to work together to identify common goals and paths moving forward. The USDA California Climate Hub and USFS Region 5 convened a symposium on drought and tree mortality in July 2017. With nearly 170 attendees across a wide range of sectors, the event provided a meaningful opportunity for reflection, analysis, and consideration of next steps. Among the outcomes of this symposium was the identification of areas in which our capacity for individual and synergistic action is stronger, and those in which it is lacking that will thus require additional attention and effort. From this symposium, which included a series of smaller, stakeholder and partner working groups, we collectively identified research and information needs, possible policy adjustments, future management actions, and funding needs and opportunities. Here, we present these findings and suggest approaches for addressing the current tree mortality event based on the shared interests of multiple, diverse stakeholder groups.

Estimating phylogenetic trees from genome-scale data.

PubMed

Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

2015-12-01

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. © 2015 New York Academy of Sciences.

Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.

PubMed

Nye, Tom M W; Tang, Xiaoxian; Weyenberg, Grady; Yoshida, Ruriko

2017-12-01

Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic analysis of gene sequences typically produces a collection of these trees, one for each gene in the analysis. Analysis of samples of trees is difficult due to the multi-dimensionality of the space of possible trees. In Euclidean spaces, principal component analysis is a popular method of reducing high-dimensional data to a low-dimensional representation that preserves much of the sample's structure. However, the space of all phylogenetic trees on a fixed set of species does not form a Euclidean vector space, and methods adapted to tree space are needed. Previous work introduced the notion of a principal geodesic in this space, analogous to the first principal component. Here we propose a geometric object for tree space similar to the [Formula: see text]th principal component in Euclidean space: the locus of the weighted Fréchet mean of [Formula: see text] vertex trees when the weights vary over the [Formula: see text]-simplex. We establish some basic properties of these objects, in particular showing that they have dimension [Formula: see text], and propose algorithms for projection onto these surfaces and for finding the principal locus associated with a sample of trees. Simulation studies demonstrate that these algorithms perform well, and analyses of two datasets, containing Apicomplexa and African coelacanth genomes respectively, reveal important structure from the second principal components.

Raman Spectroscopy an Option for the Early Detection of Citrus Huanglongbing.

PubMed

Pérez, Moisés Roberto Vallejo; Mendoza, María Guadalupe Galindo; Elías, Miguel Ghebre Ramírez; González, Francisco Javier; Contreras, Hugo Ricardo Navarro; Servín, Carlos Contreras

2016-05-01

This research describes the application of portable field Raman spectroscopy combined with a statistical analysis of the resulting spectra, employing principal component analysis (PCA) and linear discriminant analysis (LDA), in which we determine that this method provides a high degree of reliability in the early detection of Huanglongbing (HLB) on Sweet Orange, disease caused by the bacteria Candidatus Liberibacter asiaticus. Symptomatic and asymptomatic plant samples of Sweet Orange (Citrus sinensis), Persian Lime (C. latifolia), and Mexican Lime (C. aurantifolia) trees were collected from several municipalities, three at Colima State and three at Jalisco State (HLB presence). In addition, Sweet Orange samples were taken from two other Mexican municipalities, one at San Luis Potosí and the other at Veracruz (HLB absent). All samples were analyzed by real-time PCR to determine its phytosanitary condition, and its spectral signatures were obtained with an ID-Raman mini. Spectral anomalies in orange trees HLB-positive, were identified in bands related to carbohydrates (905 cm(-1), 1043 cm(-1), 1127 cm(-1), 1208 cm(-1), 1370 cm(-1), 1272 cm(-1), 1340 cm(-1), and 1260-1280 cm(-1)), amino acids, proteins (815 cm(-1), 830 cm(-1), 852 cm(-1), 918 cm(-1), 926 cm(-1), 970 cm(-1), 1002 cm(-1), 1053 cm(-1), and 1446 cm(-1)), and lipids (1734 cm(-1), 1736 cm(-1), 1738 cm(-1), 1745 cm(-1), and 1746 cm(-1)). Moreover, PCA-LDA showed a sensitivity of 86.9 % (percentage of positives, which are correctly identified), a specificity of 91.4 % (percentage of negatives, which are correctly identified), and a precision of 89.2 % (the proportion of all tests that are correct) in discriminating between orange plants HLB-positive and healthy plants. The Raman spectroscopy technique permitted rapid diagnoses, was low-cost, simple, and practical to administer, and produced immediate results. These are essential features for phytosanitary epidemiological surveillance activities that may conduct a targeted selection of highly suspicious trees to undergo molecular DNA analysis. © The Author(s) 2016.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruan, D; Shao, W; Low, D

Purpose: To evaluate and test the hypothesis that plan quality may be systematically affected by treatment delivery techniques and target-tocritical structure geometric relationship in radiotherapy for brain tumor. Methods: Thirty-four consecutive brain tumor patients treated between 2011–2014 were analyzed. Among this cohort, 10 were planned with 3DCRT, 11 with RadipArc, and 13 with helical IMRT on TomoTherapy. The selected dosimetric endpoints (i.e., PTV V100, maximum brainstem/chiasm/ optic nerve doses) were considered as a vector in a highdimensional space. A Pareto analysis was performed to identify the subset of Pareto-efficient plans.The geometric relationships, specifically the overlapping volume and centroid-of-mass distance betweenmore » each critical structure to the PTV were extracted as potential geometric features. The classification-tree analyses were repeated using these geometric features with and without the treatment modality as an additional categorical predictor. In both scenarios, the dominant features to prognosticate the Pareto membership were identified and the tree structures to provide optimal inference were recorded. The classification performance was further analyzed to determine the role of treatment modality in affecting plan quality. Results: Seven Pareto-efficient plans were identified based on dosimetric endpoints (3 from 3DCRT, 3 from RapicArc, 1 from Tomo), which implies that the evaluated treatment modality may have a minor influence on plan quality. Classification trees with/without the treatment modality as a predictor both achieved accuracy of 88.2%: with 100% sensitivity and 87.1% specificity for the former, and 66.7% sensitivity and 96.0% specificity for the latter. The coincidence of accuracy from both analyses further indicates no-to-weak dependence of plan quality on treatment modality. Both analyses have identified the brainstem to PTV distance as the primary predictive feature for Pareto-efficiency. Conclusion: Pareto evaluation and classification-tree analyses have indicated that plan quality depends strongly on geometry for brain tumor, specifically PTV-tobrain-stem-distance but minimally on treatment modality.« less

Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein.

PubMed

Tsuchiaka, Shinobu; Rahpaya, Sayed Samim; Otomaru, Konosuke; Aoki, Hiroshi; Kishimoto, Mai; Naoi, Yuki; Omatsu, Tsutomu; Sano, Kaori; Okazaki-Terashima, Sachiko; Katayama, Yukie; Oba, Mami; Nagai, Makoto; Mizutani, Tetsuya

2017-01-17

Bovine enterovirus (BEV) belongs to the species Enterovirus E or F, genus Enterovirus and family Picornaviridae. Although numerous studies have identified BEVs in the feces of cattle with diarrhea, the pathogenicity of BEVs remains unclear. Previously, we reported the detection of novel kobu-like virus in calf feces, by metagenomics analysis. In the present study, we identified a novel BEV in diarrheal feces collected for that survey. Complete genome sequences were determined by deep sequencing in feces. Secondary RNA structure analysis of the 5' untranslated region (UTR), phylogenetic tree construction and pairwise identity analysis were conducted. The complete genome sequences of BEV were genetically distant from other EVs and the VP1 coding region contained novel and unique amino acid sequences. We named this strain as BEV AN12/Bos taurus/JPN/2014 (referred to as BEV-AN12). According to genome analysis, the genome length of this virus is 7414 nucleotides excluding the poly (A) tail and its genome consists of a 5'UTR, open reading frame encoding a single polyprotein, and 3'UTR. The results of secondary RNA structure analysis showed that in the 5'UTR, BEV-AN12 had an additional clover leaf structure and small stem loop structure, similarly to other BEVs. In pairwise identity analysis, BEV-AN12 showed high amino acid (aa) identities to Enterovirus F in the polyprotein, P2 and P3 regions (aa identity ≥82.4%). Therefore, BEV-AN12 is closely related to Enterovirus F. However, aa sequences in the capsid protein regions, particularly the VP1 encoding region, showed significantly low aa identity to other viruses in genus Enterovirus (VP1 aa identity ≤58.6%). In addition, BEV-AN12 branched separately from Enterovirus E and F in phylogenetic trees based on the aa sequences of P1 and VP1, although it clustered with Enterovirus F in trees based on sequences in the P2 and P3 genome region. We identified novel BEV possessing highly divergent aa sequences in the VP1 coding region in Japan. According to species definition, we proposed naming this strain as "Enterovirus K", which is a novel species within genus Enterovirus. Further genomic studies are needed to understand the pathogenicity of BEVs.

Tree-ring reconstructions of hydroclimatic variability in the Upper Colorado River Basin

NASA Astrophysics Data System (ADS)

Hidalgo-Leon, Hugo

Three major sources of improvements in tree-ring analysis and reconstruction of hydroclimatic variables are presented for the Upper Colorado River Basin (UCRB) in the southwestern U.S.: (1) Cross validation statistics are used for identifying optimal reconstruction models based on different alternatives of PCA-based regression. Results showed that a physically-consistent parsimonious model with low mean square error can be obtained by using strict rules for principal component selection and cross validation statistics. The improved methods were used to produce a ˜500 year high-resolution reconstruction of the UCRB's streamflow and compared with results of a previous reconstruction based on traditional procedures. (2) Tree-species' type was found to be a factor for determining chronology selection from dendrohydroclimatic models. The relative sensitivity of six tree species (Pinus edulis, Pseudotsuga menziesii, Pinus ponderosa, Pinus flexilis, Pinus aristata, and Picea engelmanni) to hydroclimatic extreme variations was determined using contingency table scores of tree-ring growth (at different lags) against hydroclimatic observations. Pinus edulis and Pseudotsuga menziesii were found to be the species most sensitive to low water. Results showed that tree-rings are biased towards greater sensitivity to hot-dry conditions and less responsive to cool-moist conditions. Resulted also showed higher streamflow response scores compared to precipitation implying a good integration and persistence representation of the basin through normal hydrological processes. (3) Previous reconstructions on the basin used data extending only up to 1963. This is an important limitation since hydroclimatic records from 1963 to the present show significantly different variation than prior to 1963. The changes are caused by variations in the strength of forcing mechanisms from the Pacific Ocean. A comparative analysis of the influence of North Pacific variation and El Nino/Southern Oscillation (ENSO) showed that the responses of Tropical and North Pacific forcing in UCRB's hydroclimate are different for annual precipitation and total streamflow and that these relationships have changed at decadal time scales. Furthermore, most of the few tree-rings available up to 1985, present the same shifts as the hydroclimatic variables studied. To capture the full range of variability observed in instrumental data is necessary to collect new tree-ring samples.

Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers.

PubMed

Zhao, Lei; Annie, Ang Shi Hui; Amrita, Srivathsan; Yi, Su Kathy Feng; Rudolf, Meier

2013-10-01

We here present a phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha), a group of schizophoran flies with ca. 320 described species that is widely used in sexual selection research. The hypothesis is based on five nuclear and five mitochondrial markers totaling 8813 bp for ca. 30% of the diversity (105 sepsid taxa) and - depending on analysis - six or nine outgroup species. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian inferences (BI) yield overall congruent, well-resolved, and supported trees that are largely unaffected by three different ways to partition the data in BI and ML analyses. However, there are also five areas of uncertainty that affect suprageneric relationships where different analyses yield alternate topologies and MP and ML trees have significant conflict according to Shimodaira-Hasegawa tests. Two of these were already affected by conflict in a previous analysis that was based on the same genes and a subset of 69 species. The remaining three involve newly added taxa or genera whose relationships were previously resolved with low support. We thus find that the denser taxon sample in the present analysis does not reduce the topological conflict that had been identified previously. The present study nevertheless presents a significant contribution to the understanding of sepsid relationships in that 50 additional taxa from 18 genera are added to the Tree-of-Life of Sepsidae and that the placement of most taxa is well supported and robust to different tree reconstruction techniques. Copyright © 2013 Elsevier Inc. All rights reserved.

Widespread antisense transcription of Populus genome under drought.

PubMed

Yuan, Yinan; Chen, Su

2018-06-06

Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.

Identification, Classification and Differential Expression of Oleosin Genes in Tung Tree (Vernicia fordii)

PubMed Central

Cao, Heping; Zhang, Lin; Tan, Xiaofeng; Long, Hongxu; Shockey, Jay M.

2014-01-01

Triacylglycerols (TAG) are the major molecules of energy storage in eukaryotes. TAG are packed in subcellular structures called oil bodies or lipid droplets. Oleosins (OLE) are the major proteins in plant oil bodies. Multiple isoforms of OLE are present in plants such as tung tree (Vernicia fordii), whose seeds are rich in novel TAG with a wide range of industrial applications. The objectives of this study were to identify OLE genes, classify OLE proteins and analyze OLE gene expression in tung trees. We identified five tung tree OLE genes coding for small hydrophobic proteins. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that the five tung OLE genes represented the five OLE subfamilies and all contained the “proline knot” motif (PX5SPX3P) shared among 65 OLE from 19 tree species, including the sequenced genomes of Prunus persica (peach), Populus trichocarpa (poplar), Ricinus communis (castor bean), Theobroma cacao (cacao) and Vitis vinifera (grapevine). Tung OLE1, OLE2 and OLE3 belong to the S type and OLE4 and OLE5 belong to the SM type of Arabidopsis OLE. TaqMan and SYBR Green qPCR methods were used to study the differential expression of OLE genes in tung tree tissues. Expression results demonstrated that 1) All five OLE genes were expressed in developing tung seeds, leaves and flowers; 2) OLE mRNA levels were much higher in seeds than leaves or flowers; 3) OLE1, OLE2 and OLE3 genes were expressed in tung seeds at much higher levels than OLE4 and OLE5 genes; 4) OLE mRNA levels rapidly increased during seed development; and 5) OLE gene expression was well-coordinated with tung oil accumulation in the seeds. These results suggest that tung OLE genes 1–3 probably play major roles in tung oil accumulation and/or oil body development. Therefore, they might be preferred targets for tung oil engineering in transgenic plants. PMID:24516650

Identification, classification and differential expression of oleosin genes in tung tree (Vernicia fordii).

PubMed

Cao, Heping; Zhang, Lin; Tan, Xiaofeng; Long, Hongxu; Shockey, Jay M

2014-01-01

Triacylglycerols (TAG) are the major molecules of energy storage in eukaryotes. TAG are packed in subcellular structures called oil bodies or lipid droplets. Oleosins (OLE) are the major proteins in plant oil bodies. Multiple isoforms of OLE are present in plants such as tung tree (Vernicia fordii), whose seeds are rich in novel TAG with a wide range of industrial applications. The objectives of this study were to identify OLE genes, classify OLE proteins and analyze OLE gene expression in tung trees. We identified five tung tree OLE genes coding for small hydrophobic proteins. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that the five tung OLE genes represented the five OLE subfamilies and all contained the "proline knot" motif (PX5SPX3P) shared among 65 OLE from 19 tree species, including the sequenced genomes of Prunus persica (peach), Populus trichocarpa (poplar), Ricinus communis (castor bean), Theobroma cacao (cacao) and Vitis vinifera (grapevine). Tung OLE1, OLE2 and OLE3 belong to the S type and OLE4 and OLE5 belong to the SM type of Arabidopsis OLE. TaqMan and SYBR Green qPCR methods were used to study the differential expression of OLE genes in tung tree tissues. Expression results demonstrated that 1) All five OLE genes were expressed in developing tung seeds, leaves and flowers; 2) OLE mRNA levels were much higher in seeds than leaves or flowers; 3) OLE1, OLE2 and OLE3 genes were expressed in tung seeds at much higher levels than OLE4 and OLE5 genes; 4) OLE mRNA levels rapidly increased during seed development; and 5) OLE gene expression was well-coordinated with tung oil accumulation in the seeds. These results suggest that tung OLE genes 1-3 probably play major roles in tung oil accumulation and/or oil body development. Therefore, they might be preferred targets for tung oil engineering in transgenic plants.

Whole-tree bark and wood properties of loblolly pine from intensively managed plantations

Treesearch

Finto Antony; Laurence R. Schimleck; Richard F. Daniels; Alexander Clark; Bruce E. Borders; Michael B. Kane; Harold E. Burkhart

2015-01-01

A study was conducted to identify geographical variation in loblolly pine bark and wood properties at the whole-tree level and to quantify the responses in whole-tree bark and wood properties following contrasting silvicultural practices that included planting density, weed control, and fertilization. Trees were destructively sampled from both conventionally managed...

Prognostic Factors and Decision Tree for Long-term Survival in Metastatic Uveal Melanoma.

PubMed

Lorenzo, Daniel; Ochoa, María; Piulats, Josep Maria; Gutiérrez, Cristina; Arias, Luis; Català, Jaum; Grau, María; Peñafiel, Judith; Cobos, Estefanía; Garcia-Bru, Pere; Rubio, Marcos Javier; Padrón-Pérez, Noel; Dias, Bruno; Pera, Joan; Caminal, Josep Maria

2017-12-04

The purpose of this study was to demonstrate the existence of a bimodal survival pattern in metastatic uveal melanoma. Secondary aims were to identify the characteristics and prognostic factors associated with long-term survival and to develop a clinical decision tree. The medical records of 99 metastatic uveal melanoma patients were retrospectively reviewed. Patients were classified as either short (≤ 12 months) or long-term survivors (> 12 months) based on a graphical interpretation of the survival curve after diagnosis of the first metastatic lesion. Ophthalmic and oncological characteristics were assessed in both groups. Of the 99 patients, 62 (62.6%) were classified as short-term survivors, and 37 (37.4%) as long-term survivors. The multivariate analysis identified the following predictors of long-term survival: age ≤ 65 years (p=0.012) and unaltered serum lactate dehydrogenase levels (p=0.018); additionally, the size (smaller vs. larger) of the largest liver metastasis showed a trend towards significance (p=0.063). Based on the variables significantly associated with long-term survival, we developed a decision tree to facilitate clinical decision-making. The findings of this study demonstrate the existence of a bimodal survival pattern in patients with metastatic uveal melanoma. The presence of certain clinical characteristics at diagnosis of distant disease is associated with long-term survival. A decision tree was developed to facilitate clinical decision-making and to counsel patients about the expected course of disease.

Quantifying pruning impacts on olive tree architecture and annual canopy growth by using UAV-based 3D modelling.

PubMed

Jiménez-Brenes, F M; López-Granados, F; de Castro, A I; Torres-Sánchez, J; Serrano, N; Peña, J M

2017-01-01

Tree pruning is a costly practice with important implications for crop harvest and nutrition, pest and disease control, soil protection and irrigation strategies. Investigations on tree pruning usually involve tedious on-ground measurements of the primary tree crown dimensions, which also might generate inconsistent results due to the irregular geometry of the trees. As an alternative to intensive field-work, this study shows a innovative procedure based on combining unmanned aerial vehicle (UAV) technology and advanced object-based image analysis (OBIA) methodology for multi-temporal three-dimensional (3D) monitoring of hundreds of olive trees that were pruned with three different strategies (traditional, adapted and mechanical pruning). The UAV images were collected before pruning, after pruning and a year after pruning, and the impacts of each pruning treatment on the projected canopy area, tree height and crown volume of every tree were quantified and analyzed over time. The full procedure described here automatically identified every olive tree on the orchard and computed their primary 3D dimensions on the three study dates with high accuracy in the most cases. Adapted pruning was generally the most aggressive treatment in terms of the area and volume (the trees decreased by 38.95 and 42.05% on average, respectively), followed by trees under traditional pruning (33.02 and 35.72% on average, respectively). Regarding the tree heights, mechanical pruning produced a greater decrease (12.15%), and these values were minimal for the other two treatments. The tree growth over one year was affected by the pruning severity and by the type of pruning treatment, i.e., the adapted-pruning trees experienced higher growth than the trees from the other two treatments when pruning intensity was low (<10%), similar to the traditionally pruned trees at moderate intensity (10-30%), and lower than the other trees when the pruning intensity was higher than 30% of the crown volume. Combining UAV-based images and an OBIA procedure allowed measuring tree dimensions and quantifying the impacts of three different pruning treatments on hundreds of trees with minimal field work. Tree foliage losses and annual canopy growth showed different trends as affected by the type and severity of the pruning treatments. Additionally, this technology offers valuable geo-spatial information for designing site-specific crop management strategies in the context of precision agriculture, with the consequent economic and environmental benefits.

Ortholog-based screening and identification of genes related to intracellular survival.

PubMed

Yang, Xiaowen; Wang, Jiawei; Bing, Guoxia; Bie, Pengfei; De, Yanyan; Lyu, Yanli; Wu, Qingmin

2018-04-20

Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes. In this study, the genes of common pathogens were analyzed to screen and identify genes associated with intracellular survival through sequence similarity, phylogenetic tree analysis and the λ-Red recombination system test method. The total 38,952 protein-coding genes of common pathogens were divided into 19,775 clusters. As demonstrated through a COG analysis, information storage and processing genes might play an important role intracellular survival. Only 19 clusters were present in facultative intracellular pathogens, and not all were present in extracellular pathogens. Construction of a phylogenetic tree selected 18 of these 19 clusters. Comparisons with the DEG database and previous research revealed that seven other clusters are considered essential gene clusters and that seven other clusters are associated with intracellular survival. Moreover, this study confirmed that clusters screened by orthologs with similar function could be replaced with an approved uvrY gene and its orthologs, and the results revealed that the usg gene is associated with intracellular survival. The study improves the current understanding of intracellular pathogens characteristics and allows further exploration of the intracellular survival-related gene modules in these pathogens. Copyright © 2018. Published by Elsevier B.V.

Epigenetic Variability in the Genetically Uniform Forest Tree Species Pinus pinea L

PubMed Central

Sáez-Laguna, Enrique; Guevara, María-Ángeles; Díaz, Luis-Manuel; Sánchez-Gómez, David; Collada, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-01-01

There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees. PMID:25084460

Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

PubMed

Sáez-Laguna, Enrique; Guevara, María-Ángeles; Díaz, Luis-Manuel; Sánchez-Gómez, David; Collada, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-01-01

There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

FORAST Database: Forest Responses to Anthropogenic Stress (FORAST)

DOE Data Explorer

McLaughlin, S. B. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Downing, D. J. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Blasing, T. J. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Jackson, B. L. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Pack, D. J. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Duvick, D. N. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Mann, L. K. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Doyle, T. W. [ESD, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA)

1995-01-01

The Forest Responses to Anthropogenic Stress (FORAST) project was designed to determine whether evidence of alterations of long-term growth patterns of several species of eastern forest trees was apparent in tree-ring chronologies from within the region and to identify environmental variables that were temporally or spatially correlated with any observed changes. The project was supported principally by the U.S. Environmental Protection Agency (EPA) with additional support from the National Park Service. The FORAST project was initiated in 1982 as exploratory research to document patterns of radial growth of forest trees during the previous 50 or more years within 15 states in the northeastern United States. Radial growth measurements from more than 7,000 trees are provided along with data on a variety of measured and calculated indices of stand characteristics (basal area, density, and competitive indices); climate (temperature, precipitation, and drought); and anthropogenic pollutants (state and regional emissions of SO2 and NOX, ozone monitoring data, and frequency of atmospheric-stagnation episodes and atmospheric haze). These data were compiled into a single database to facilitate exploratory analysis of tree growth patterns and responses to local and regional environmental conditions. The project objectives, experimental design, and documentation of procedures for assessing data collected in the 3-year research project are reported in McLaughlin et al. (1986).

Studying global change through investigation of the plastic responses of xylem anatomy in tree rings.

PubMed

Fonti, Patrick; von Arx, Georg; García-González, Ignacio; Eilmann, Britta; Sass-Klaassen, Ute; Gärtner, Holger; Eckstein, Dieter

2010-01-01

Variability in xylem anatomy is of interest to plant scientists because of the role water transport plays in plant performance and survival. Insights into plant adjustments to changing environmental conditions have mainly been obtained through structural and functional comparative studies between taxa or within taxa on contrasting sites or along environmental gradients. Yet, a gap exists regarding the study of hydraulic adjustments in response to environmental changes over the lifetimes of plants. In trees, dated tree-ring series are often exploited to reconstruct dynamics in ecological conditions, and recent work in which wood-anatomical variables have been used in dendrochronology has produced promising results. Environmental signals identified in water-conducting cells carry novel information reflecting changes in regional conditions and are mostly related to short, sub-annual intervals. Although the idea of investigating environmental signals through wood anatomical time series goes back to the 1960s, it is only recently that low-cost computerized image-analysis systems have enabled increased scientific output in this field. We believe that the study of tree-ring anatomy is emerging as a promising approach in tree biology and climate change research, particularly if complemented by physiological and ecological studies. This contribution presents the rationale, the potential, and the methodological challenges of this innovative approach.

Hybrid Parallel Contour Trees, Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sewell, Christopher; Fasel, Patricia; Carr, Hamish

A common operation in scientific visualization is to compute and render a contour of a data set. Given a function of the form f : R^d -> R, a level set is defined as an inverse image f^-1(h) for an isovalue h, and a contour is a single connected component of a level set. The Reeb graph can then be defined to be the result of contracting each contour to a single point, and is well defined for Euclidean spaces or for general manifolds. For simple domains, the graph is guaranteed to be a tree, and is called the contourmore » tree. Analysis can then be performed on the contour tree in order to identify isovalues of particular interest, based on various metrics, and render the corresponding contours, without having to know such isovalues a priori. This code is intended to be the first data-parallel algorithm for computing contour trees. Our implementation will use the portable data-parallel primitives provided by Nvidia’s Thrust library, allowing us to compile our same code for both GPUs and multi-core CPUs. Native OpenMP and purely serial versions of the code will likely also be included. It will also be extended to provide a hybrid data-parallel / distributed algorithm, allowing scaling beyond a single GPU or CPU.« less

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

PubMed Central

2012-01-01

Background In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development. Results In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO) and Clusters of Orthologous Group (COG). When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%), suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study. Conclusion By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research generated a substantial fraction of rubber tree transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation, and microarrays development in rubber tree. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding in rubber tree. Moreover, this study also supported that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for transcriptome characterization and molecular marker development in non-model species, especially those with large and complex genomes. PMID:22607098

Modeling individual trees in an urban environment using dense discrete return LIDAR

NASA Astrophysics Data System (ADS)

Bandyopadhyay, Madhurima; van Aardt, Jan A. N.; van Leeuwen, Martin

2015-05-01

The urban forest is becoming increasingly important in the contexts of urban green space, carbon sequestration and offsets, and socio-economic impacts. This has led to a recent increase in attention being paid to urban environmental management. Tree biomass, specifically, is a vital indicator of carbon storage and has a direct impact on urban forest health and carbon sequestration. As an alternative to expensive and time-consuming field surveys, remote sensing has been used extensively in measuring dynamics of vegetation and estimating biomass. Light detection and ranging (LiDAR) has proven especially useful to characterize the three dimensional (3D) structure of forests. In urban contexts however, information is frequently required at the individual tree level, necessitating the proper delineation of tree crowns. Yet, crown delineation is challenging for urban trees where a wide range of stress factors and cultural influences affect growth. In this paper high resolution LiDAR data were used to infer biomass based on individual tree attributes. A multi-tiered delineation algorithm was designed to extract individual tree-crowns. At first, dominant tree segments were obtained by applying watershed segmentation on the crown height model (CHM). Next, prominent tree top positions within each segment were identified via a regional maximum transformation and the crown boundary was estimated for each of the tree tops. Finally, undetected trees were identified using a best-fitting circle approach. After tree delineation, individual tree attributes were used to estimate tree biomass and the results were validated with associated field mensuration data. Results indicate that the overall tree detection accuracy is nearly 80%, and the estimated biomass model has an adjusted-R2 of 0.5.

"Mad or bad?": burden on caregivers of patients with personality disorders.

PubMed

Bauer, Rita; Döring, Antje; Schmidt, Tanja; Spießl, Hermann

2012-12-01

The burden on caregivers of patients with personality disorders is often greatly underestimated or completely disregarded. Possibilities for caregiver support have rarely been assessed. Thirty interviews were conducted with caregivers of such patients to assess illness-related burden. Responses were analyzed with a mixed method of qualitative and quantitative analysis in a sequential design. Patient and caregiver data, including sociodemographic and disease-related variables, were evaluated with regression analysis and regression trees. Caregiver statements (n = 404) were summarized into 44 global statements. The most frequent global statements were worries about the burden on other family members (70.0%), poor cooperation with clinical centers and other institutions (60.0%), financial burden (56.7%), worry about the patient's future (53.3%), and dissatisfaction with the patient's treatment and rehabilitation (53.3%). Linear regression and regression tree analysis identified predictors for more burdened caregivers. Caregivers of patients with personality disorders experience a variety of burdens, some disorder specific. Yet these caregivers often receive little attention or support.

Basic Helix-Loop-Helix Transcription Factor Gene Family Phylogenetics and Nomenclature

PubMed Central

Skinner, Michael K.; Rawls, Alan; Wilson-Rawls, Jeanne; Roalson, Eric H.

2010-01-01

A phylogenetic analysis of the basic helix-loop-helix (bHLH) gene superfamily was performed using seven different species (human, mouse, rat, worm, fly, yeast, and plant Arabidopsis) and involving over 600 bHLH genes [1]. All bHLH genes were identified in the genomes of the various species, including expressed sequence tags, and the entire coding sequence was used in the analysis. Nearly 15% of the gene family has been updated or added since the original publication. A super-tree involving six clades and all structural relationships was established and is now presented for four of the species. The wealth of functional data available for members of the bHLH gene superfamily provides us with the opportunity to use this exhaustive phylogenetic tree to predict potential functions of uncharacterized members of the family. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique elements of the evolution and functional relationships of the different genes in the bHLH gene family. PMID:20219281

Economic analysis of emerald ash borer (Coleoptera: Buprestidae) management options.

PubMed

Vannatta, A R; Hauer, R H; Schuettpelz, N M

2012-02-01

Emerald ash borer, Agrilus planipennis (Fairmaire) (Coleoptera: Buprestidae), plays a significant role in the health and extent of management of native North American ash species in urban forests. An economic analysis of management options was performed to aid decision makers in preparing for likely future infestations. Separate ash tree population valuations were derived from the i-Tree Streets program and the Council of Tree and Landscape Appraisers (CTLA) methodology. A relative economic analysis was used to compare a control option (do-nothing approach, only removing ash trees as they die) to three distinct management options: 1) preemptive removal of all ash trees over a 5 yr period, 2) preemptive removal of all ash trees and replacement with comparable nonash trees, or 3) treating the entire population of ash trees with insecticides to minimize mortality. For each valuation and management option, an annual analysis was performed for both the remaining ash tree population and those lost to emerald ash borer. Retention of ash trees using insecticide treatments typically retained greater urban forest value, followed by doing nothing (control), which was better than preemptive removal and replacement. Preemptive removal without tree replacement, which was the least expensive management option, also provided the lowest net urban forest value over the 20-yr simulation. A "no emerald ash borer" scenario was modeled to further serve as a benchmark for each management option and provide a level of economic justification for regulatory programs aimed at slowing the movement of emerald ash borer.

Application of ISO22000, failure mode, and effect analysis (FMEA) cause and effect diagrams and pareto in conjunction with HACCP and risk assessment for processing of pastry products.

PubMed

Varzakas, Theodoros H

2011-09-01

The Failure Mode and Effect Analysis (FMEA) model has been applied for the risk assessment of pastry processing. A tentative approach of FMEA application to the pastry industry was attempted in conjunction with ISO22000. Preliminary Hazard Analysis was used to analyze and predict the occurring failure modes in a food chain system (pastry processing plant), based on the functions, characteristics, and/or interactions of the ingredients or the processes, upon which the system depends. Critical Control points have been identified and implemented in the cause and effect diagram (also known as Ishikawa, tree diagram, and fishbone diagram). In this work a comparison of ISO22000 analysis with HACCP is carried out over pastry processing and packaging. However, the main emphasis was put on the quantification of risk assessment by determining the Risk Priority Number (RPN) per identified processing hazard. Storage of raw materials and storage of final products at -18°C followed by freezing were the processes identified as the ones with the highest RPN (225, 225, and 144 respectively) and corrective actions were undertaken. Following the application of corrective actions, a second calculation of RPN values was carried out leading to considerably lower values (below the upper acceptable limit of 130). It is noteworthy that the application of Ishikawa (Cause and Effect or Tree diagram) led to converging results thus corroborating the validity of conclusions derived from risk assessment and FMEA. Therefore, the incorporation of FMEA analysis within the ISO22000 system of a pastry processing industry is considered imperative.

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life.

PubMed

Verbruggen, Heroen; Maggs, Christine A; Saunders, Gary W; Le Gall, Line; Yoon, Hwan Su; De Clerck, Olivier

2010-01-20

The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them. Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches. Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Evaluating phylogenetic congruence in the post-genomic era.

PubMed

Leigh, Jessica W; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.

Evaluating Phylogenetic Congruence in the Post-Genomic Era

PubMed Central

Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

Epidemiologic Trends in Medically-attended Tree Stand Fall Injuries among Wisconsin Deer Hunters

PubMed Central

VanWormer, Jeffrey J.; Holsman, Robert H.; Petchenik, Jordan B.; Dhuey, Brian J.; Keifer, Matthew C.

2015-01-01

Background Tree stand falls are the most common injury to hunters in the USA, but there is limited research on the topic. This study examined the 5-year trends in incident tree stand fall injuries in rural north-central Wisconsin and described patient demographics and injury features. Methods A retrospective analysis was conducted on five prior hunting seasons, 2009–2013. Cases were ascertained from electronic health records via natural language processing that identified patients from the Marshfield Epidemiologic Study Area who received medical attention for a tree stand fall. Annual incidence rates were calculated using the number of hunting license holders in the target population, per administrative data from the Wisconsin Department of Natural Resources. Results There were 16,556–16,902 deer hunters in any given year, with 39 (92% male) confirmed medically-attended tree stand fall injuries in 2009–2013. Injuries mainly occurred in the lower extremities (n=23), and included two fatalities and one paralysis case. The risk of tree stand fall injuries went from 6.0 (95% CI: 3.2, 11.1) per 10,000 hunters in 2009 to 3.6 (95% CI: 1.6, 7.9) per 10,000 hunters in 2013, which was not a significant change over five years (p=0.79). Most falls occurred among archery hunters, in the evening and when descending from a tree stand. Cases were demographically similar to the general population of Wisconsin deer hunters. Conclusions The current seasonal incidence rate of tree stand fall injuries is relatively low in rural Wisconsin, but with limited signs of improvement. Continued efforts are needed to promote the long-term safety of the hunting public. PMID:26443558

Epidemiologic trends in medically-attended tree stand fall injuries among Wisconsin deer hunters.

PubMed

VanWormer, Jeffrey J; Holsman, Robert H; Petchenik, Jordan B; Dhuey, Brian J; Keifer, Matthew C

2016-01-01

Tree stand falls are the most common injury to hunters in the USA, but there is limited research on the topic. This study examined the 5-year trends in incident tree stand fall injuries in rural north-central Wisconsin and described patient demographics and injury features. A retrospective analysis was conducted on five prior hunting seasons, 2009-2013. Cases were ascertained from electronic health records via natural language processing that identified patients from the Marshfield Epidemiologic Study Area who received medical attention for a tree stand fall. Annual incidence rates were calculated using the number of hunting license holders in the target population, per administrative data from the Wisconsin Department of Natural Resources. There were 16,556-16,902 deer hunters in any given year, with 39 (92% male) confirmed medically-attended tree stand fall injuries in 2009-2013. Injuries mainly occurred in the lower extremities (n=23), and included two fatalities and one paralysis case. The risk of tree stand fall injuries went from 6.0 (95% CI: 3.2, 11.1) per 10,000 hunters in 2009 to 3.6 (95% CI: 1.6, 7.9) per 10,000 hunters in 2013, which was not a significant change over 5 years (p=0.79). Most falls occurred among archery hunters, in the evening and when descending from a tree stand. Cases were demographically similar to the general population of Wisconsin deer hunters. The current seasonal incidence rate of tree stand fall injuries is relatively low in rural Wisconsin, but with limited signs of improvement. Continued efforts are needed to promote the long-term safety of the hunting public. Copyright © 2015 Elsevier Ltd. All rights reserved.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

The sweet side of global change-dynamic responses of non-structural carbohydrates to drought, elevated CO2 and nitrogen fertilization in tree species.

PubMed

Li, Weibin; Hartmann, Henrik; Adams, Henry D; Zhang, Hongxia; Jin, Changjie; Zhao, Chuanyan; Guan, Dexin; Wang, Anzhi; Yuan, Fenghui; Wu, Jiabing

2018-06-11

Non-structural carbohydrates (NSC) play a central role in plant functioning as energy carriers and building blocks for primary and secondary metabolism. Many studies have investigated how environmental and anthropogenic changes, like increasingly frequent and severe drought episodes, elevated CO2 and atmospheric nitrogen (N) deposition, influence NSC concentrations in individual trees. However, this wealth of data has not been analyzed yet to identify general trends using a common statistical framework. A thorough understanding of tree responses to global change is required for making realistic predictions of vegetation dynamics. Here we compiled data from 57 experimental studies on 71 tree species and conducted a meta-analysis to evaluate general responses of stored soluble sugars, starch and total NSC (soluble sugars + starch) concentrations in different tree organs (foliage, above-ground wood and roots) to drought, elevated CO2 and N deposition. We found that drought significantly decreased total NSC in roots (-17.3%), but not in foliage and above-ground woody tissues (bole, branch, stem and/or twig). Elevated CO2 significantly increased total NSC in foliage (+26.2%) and roots (+12.8%), but not in above-ground wood. By contrast, total NSC significantly decreased in roots (-17.9%), increased in above-ground wood (+6.1%), but was unaffected in foliage from N fertilization. In addition, the response of NSC to three global change drivers was strongly affected by tree taxonomic type, leaf habit, tree age and treatment intensity. Our results pave the way for a better understanding of general tree function responses to drought, elevated CO2 and N fertilization. The existing data also reveal that more long-term studies on mature trees that allow testing interactions between these factors are urgently needed to provide a basis for forecasting tree responses to environmental change at the global scale.

Tree Rings as Chroniclers of Mercury Exposure in Shenandoah National Park, Virginia

NASA Astrophysics Data System (ADS)

Riscassi, A. L.; Camper, T.; Lee, T. R.; Druckenbrod, D.; Scanlon, T. M.

2016-12-01

Although historical Hg emissions and subsequent deposition play a dominant role in shaping present and future Hg cycling, our knowledge of this is limited in both space and time. Recent studies have shown Hg concentrations in tree rings have the potential to archive historical Hg exposure from local, regional, and global sources, however, no studies have evaluated tree rings in the eastern U.S., a region of elevated Hg deposition from upwind power plants. In order to chronicle the historical Hg exposure of the central Appalachian region through dendrochemical analysis, tree rings were cored along a latitudinal gradient in Shenandoah National Park with sites clustered in North, Central and Southern regions. Long-lived tree species with low radial permeability, chosen to avoid the potential for chemical translocation, included white oak (Quercus Alba), northern red oak (Quercus rubra), and pitch pine (Pinus rigida). In each of the three regions, we collected a core from three individuals of each tree species (27 total cores) and analyzed each for Hg content in 10-yr increments. Overall, tree ring Hg concentrations (average 0.88 ng Hg g-1) were similar to other studies and varied between species. Temporal tree-core Hg trends did not relate to trends in modeled global atmospheric Hg concentrations or regional sources (e.g., fire, coal production), but rather tracked the use of Hg from a local industrial point source. Contemporary wind data originating from the location of the local Hg source in conjunction with an atmospheric model indicate emissions from the plant likely impact the southern region of the park, with a lesser influence in the central and north regions, matching the longitudinal gradient observed in tree rings. This study raises questions about the extent of historical contamination from the industrial site and demonstrates the potential usefulness of tree ring dendrochemistry for identifying historical sources of atmospheric Hg exposure.

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data.

PubMed

Lee, Tae-Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H

2014-02-26

Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data. We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline. Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.

Risk management of PPP project in the preparation stage based on Fault Tree Analysis

NASA Astrophysics Data System (ADS)

Xing, Yuanzhi; Guan, Qiuling

2017-03-01

The risk management of PPP(Public Private Partnership) project can improve the level of risk control between government departments and private investors, so as to make more beneficial decisions, reduce investment losses and achieve mutual benefit as well. Therefore, this paper takes the PPP project preparation stage venture as the research object to identify and confirm four types of risks. At the same time, fault tree analysis(FTA) is used to evaluate the risk factors that belong to different parts, and quantify the influencing degree of risk impact on the basis of risk identification. In addition, it determines the importance order of risk factors by calculating unit structure importance on PPP project preparation stage. The result shows that accuracy of government decision-making, rationality of private investors funds allocation and instability of market returns are the main factors to generate the shared risk on the project.

Polymorphism and selection in the major histocompatibility complex DRA and DQA genes in the family Equidae.

PubMed

Janova, Eva; Matiasovic, Jan; Vahala, Jiri; Vodicka, Roman; Van Dyk, Enette; Horin, Petr

2009-07-01

The major histocompatibility complex genes coding for antigen binding and presenting molecules are the most polymorphic genes in the vertebrate genome. We studied the DRA and DQA gene polymorphism of the family Equidae. In addition to 11 previously reported DRA and 24 DQA alleles, six new DRA sequences and 13 new DQA alleles were identified in the genus Equus. Phylogenetic analysis of both DRA and DQA sequences provided evidence for trans-species polymorphism in the family Equidae. The phylogenetic trees differed from species relationships defined by standard taxonomy of Equidae and from trees based on mitochondrial or neutral gene sequence data. Analysis of selection showed differences between the less variable DRA and more variable DQA genes. DRA alleles were more often shared by more species. The DQA sequences analysed showed strong amongst-species positive selection; the selected amino acid positions mostly corresponded to selected positions in rodent and human DQA genes.

Binary partition tree analysis based on region evolution and its application to tree simplification.

PubMed

Lu, Huihai; Woods, John C; Ghanbari, Mohammed

2007-04-01

Pyramid image representations via tree structures are recognized methods for region-based image analysis. Binary partition trees can be applied which document the merging process with small details found at the bottom levels and larger ones close to the root. Hindsight of the merging process is stored within the tree structure and provides the change histories of an image property from the leaf to the root node. In this work, the change histories are modelled by evolvement functions and their second order statistics are analyzed by using a knee function. Knee values show the reluctancy of each merge. We have systematically formulated these findings to provide a novel framework for binary partition tree analysis, where tree simplification is demonstrated. Based on an evolvement function, for each upward path in a tree, the tree node associated with the first reluctant merge is considered as a pruning candidate. The result is a simplified version providing a reduced solution space and still complying with the definition of a binary tree. The experiments show that image details are preserved whilst the number of nodes is dramatically reduced. An image filtering tool also results which preserves object boundaries and has applications for segmentation.

Alaska Is Our Home--Book 3: A Natural Science Handbook for Alaskan Students.

ERIC Educational Resources Information Center

Bury, John; Bury, Susan

The third book in a series of natural science handbooks for Alaskan students focuses on Alaskan plantlife. The first chapter, on trees, gives general information about trees and explains how to identify and locate trees in the three main Alaskan tree families: pine, willow, and birch. The second chapter, on plants, describes 14 kinds of edible…

Water uptake of trees in a montane forest catchment and the geomorphological potential of root growth in Boulder Creek Critical Zone Observatory, Rocky Mountains, Colorado

NASA Astrophysics Data System (ADS)

Skeets, B.; Barnard, H. R.; Byers, A.

2011-12-01

The influence of vegetation on the hydrological cycle and the possible effect of roots in geomorphological processes are poorly understood. Gordon Gulch watershed in the Front Range of the Rocky Mountains, Colorado, is a montane climate ecosystem of the Boulder Creek Critical Zone Observatory whose study adds to the database of ecohydrological work in different climates. This work sought to identify the sources of water used by different tree species and to determine how trees growing in rock outcrops may contribute to the fracturing and weathering of rock. Stable isotopes (18O and 2H) were analyzed from water extracted from soil and xylem samples. Pinus ponderosa on the south-facing slope consumes water from deeper depths during dry periods and uses newly rain-saturated soils, after rainfall events. Pinus contorta on the north -facing slope shows a similar, expected response in water consumption, before and after rain. Two trees (Pinus ponderosa) growing within rock outcrops demonstrate water use from cracks replenished by new rains. An underexplored question in geomorphology is whether tree roots growing in rock outcrops contribute to long-term geomorphological processes by physically deteriorating the bedrock. The dominant roots of measured trees contributed approximately 30 - 80% of total water use, seen especially after rainfall events. Preliminary analysis of root growth rings indicates that root growth is capable of expanding rock outcrop fractures at an approximate rate of 0.6 - 1.0 mm per year. These results demonstrate the significant role roots play in tree physiological processes and in bedrock deterioration.

Reducing Uncertainty in Transpiration Estimation in Wet Tropical Forests and Upscaling Sap Flux Measurements in Complex Heterogeneous Systems

NASA Astrophysics Data System (ADS)

Moore, G. W.; Aparecido, L. M. T.; Jaimes, A.

2017-12-01

High tree species and functional diversity, complex age and stand structure, deeper active sapwood, and potential factors that reduce transpiration, such as frequent cloud cover and wet leaves are inherent in wet tropical forests. In face of these unique challenges, advancements are needed for optimizing in situ measurement strategies to reduce uncertainties, in particular, within-tree and among-tree variation. Over a five-year period, we instrumented 44 trees with heat dissipation sap flow sensors within a premontane wet tropical rainforest in Costa Rica (5000 mm MAP). Sensors were systematically apportioned among overstory, midstory, and suppressed trees. In a subset of dominant trees, radial profiles across the full range of active xylem were fitted as deep as 16 cm. Given high diversity, few instrumented trees belonged to the same species, genus, or even family. Leaf surfaces were wet 20-80% of daylight hours from the top to bottom of the canopy, respectively. As a result, transpiration was suppressed, even after accounting for lower vapor pressure deficit (<0.5 kPa) and reduced solar radiation (<500 W m-1). To the contrary, the driest month on record resulted in higher, not lower transpiration. We identified multiple functional types according to patterns in dry season water use for the period February to April, 2016 using Random Forest analysis to discriminate groups with unique temporal responses. These efforts are critical for improving global land surface models that increasingly partition canopy components within complex heterogeneous systems, and for improved accuracy of transpiration estimates in tropical forests.

Molecular and genetic regulation of tree branch orientation

USDA-ARS?s Scientific Manuscript database

The ability to genetically manipulate tree form can significantly benefit orchard and tree plantation management by enabling higher density plantings, mechanized harvesting, and reduce both chemical use and costly manual labor. Using both Prunus persica and Arabidopsis thaliana, we identified an an...

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

PubMed

Timme, Ruth E; Rand, Hugh; Shumway, Martin; Trees, Eija K; Simmons, Mustafa; Agarwala, Richa; Davis, Steven; Tillman, Glenn E; Defibaugh-Chavez, Stephanie; Carleton, Heather A; Klimke, William A; Katz, Lee S

2017-01-01

As next generation sequence technology has advanced, there have been parallel advances in genome-scale analysis programs for determining evolutionary relationships as proxies for epidemiological relationship in public health. Most new programs skip traditional steps of ortholog determination and multi-gene alignment, instead identifying variants across a set of genomes, then summarizing results in a matrix of single-nucleotide polymorphisms or alleles for standard phylogenetic analysis. However, public health authorities need to document the performance of these methods with appropriate and comprehensive datasets so they can be validated for specific purposes, e.g., outbreak surveillance. Here we propose a set of benchmark datasets to be used for comparison and validation of phylogenomic pipelines. We identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches). These are ideal benchmark datasets, as the trees, WGS data, and epidemiological data for each are all in agreement. We have placed these sequence data, sample metadata, and "known" phylogenetic trees in publicly-accessible databases and developed a standard descriptive spreadsheet format describing each dataset. To facilitate easy downloading of these benchmarks, we developed an automated script that uses the standard descriptive spreadsheet format. Our "outbreak" benchmark datasets represent the four major foodborne bacterial pathogens ( Listeria monocytogenes , Salmonella enterica , Escherichia coli , and Campylobacter jejuni ) and one simulated dataset where the "known tree" can be accurately called the "true tree". The downloading script and associated table files are available on GitHub: https://github.com/WGS-standards-and-analysis/datasets. These five benchmark datasets will help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations. Our work is part of a global effort to provide collaborative infrastructure for sequence data and analytic tools-we welcome additional benchmark datasets in our recommended format, and, if relevant, we will add these on our GitHub site. Together, these datasets, dataset format, and the underlying GitHub infrastructure present a recommended path for worldwide standardization of phylogenomic pipelines.

Monte Carlo Simulation of Markov, Semi-Markov, and Generalized Semi- Markov Processes in Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

English, Thomas

2005-01-01

A standard tool of reliability analysis used at NASA-JSC is the event tree. An event tree is simply a probability tree, with the probabilities determining the next step through the tree specified at each node. The nodal probabilities are determined by a reliability study of the physical system at work for a particular node. The reliability study performed at a node is typically referred to as a fault tree analysis, with the potential of a fault tree existing.for each node on the event tree. When examining an event tree it is obvious why the event tree/fault tree approach has been adopted. Typical event trees are quite complex in nature, and the event tree/fault tree approach provides a systematic and organized approach to reliability analysis. The purpose of this study was two fold. Firstly, we wanted to explore the possibility that a semi-Markov process can create dependencies between sojourn times (the times it takes to transition from one state to the next) that can decrease the uncertainty when estimating time to failures. Using a generalized semi-Markov model, we studied a four element reliability model and were able to demonstrate such sojourn time dependencies. Secondly, we wanted to study the use of semi-Markov processes to introduce a time variable into the event tree diagrams that are commonly developed in PRA (Probabilistic Risk Assessment) analyses. Event tree end states which change with time are more representative of failure scenarios than are the usual static probability-derived end states.

Global Tree Range Shifts Under Forecasts from Two Alternative GCMs Using Two Future Scenarios

NASA Astrophysics Data System (ADS)

Hargrove, W. W.; Kumar, J.; Potter, K. M.; Hoffman, F. M.

2013-12-01

Global shifts in the environmentally suitable ranges of 215 tree species were predicted under forecasts from two GCMs (the Parallel Climate Model (PCM), and the Hadley Model), each under two IPCC future climatic scenarios (A1 and B1), each at two future dates (2050 and 2100). The analysis considers all global land surface at a resolution of 4 km2. A statistical multivariate clustering procedure was used to quantitatively delineate 30 thousand environmentally homogeneous ecoregions across present and 8 potential future global locations at once, using global maps of 17 environmental characteristics describing temperature, precipitation, soils, topography and solar insolation. Presence of each tree species on Forest Inventory Analysis (FIA) plots and in Global Biodiversity Information Facility (GBIF) samples was used to select a subset of suitable ecoregions from the full set of 30 thousand. Once identified, this suitable subset of ecoregions was compared to the known current range of the tree species under present conditions. Predicted present ranges correspond well with current understanding for all but a few of the 215 tree species. The subset of suitable ecoregions for each tree species can then be tracked into the future to determine whether the suitable home range for this species remains the same, moves, grows, shrinks, or disappears under each model/scenario combination. Occurrence and growth performance measurements for various tree species across the U.S. are limited to FIA plots. We present a new, general-purpose empirical imputation method which associates sparse measurements of dependent variables with particular multivariate clustered combinations of the independent variables, and then estimates values for unmeasured clusters, based on directional proximity in multidimensional data space, at both the cluster and map-cell levels of resolution. Using Associative Clustering, we scaled up the FIA point measurements into contonuous maps that show the expected growth and suitability for individual tree species across the continental US. Maps were generated for each tree species showing the Minimum Required Movement (MRM) straight-line distance from each currently suitable location to the geographically nearest "lifeboat" location having suitable conditions in the future. Locations that are the closest "lifeboats" for many MRM propagules originating from wide surrounding areas may constitute high-priority preservation targets as a refugium against climatic change.

Ornamental Planting Restoration at Jefferson's Poplar Forest Through XRF and ICP-OES Analysis of Disturbed Soils

NASA Astrophysics Data System (ADS)

Hatfield, M.; Low, P. C.; Devlin, S.

2011-12-01

Thomas Jefferson's Poplar Forest estate near Lynchburg, VA is currently attempting to restore the property to its Jeffersonian condition. Subsequent modifications to the property following its sale by Jefferson's heirs included the removal of the original trees in order to facilitate agricultural activity. One key facet of the restoration involves determining the precise location of the sixty-four paper mulberry trees that Jefferson reportedly had transplanted in 1815 from his on-site nursery to near the main house. At Monticello, it is well-documented that Jefferson used contextually innovative fertilizing techniques, including the addition of gypsum and lime "to restore the exhaustion of a single crop from the soil." Whether he used these methods in the nursery at Poplar Forest to the degree that decades of subsequent leaching, weathering, and other disturbances would not erase remains historically and analytically unclear. Since the transplantation process requires that large amounts of soil be moved with the trees, small areas of compositionally distinct soils in the suspected planting area could be used to establish the exact location of each tree through differentiating between nursery and in situ soils. Through X-ray fluorescence spectroscopy (XRF) and intercoupled plasma optical emission spectroscopy (ICP-OES) geochemical analysis, the specific composition of soil can be determined. Preliminary analysis shows slight differences in phosphorus and sulfur between the nursery and in situ soil; however, the property lies on three different distinct geological units: actinolite schist and feldspathic metagreywacke units of the Alligator Back formation, and biotite gneiss of the Ashe Formation (biotite gneiss). The location of the nursery where the sixty-four paper mulberry trees were originally grown lies on the feldspathic metagreywacke unit; whereas the relocation site where Jefferson had them planted rests on the actinolite schist unit. Percursory study identifies significant differences in major elements such as silicon, aluminum, calcium, and manganese. Locating the presence of the nursery soil within the relocation site soil will allow staff archaeologists to replant the paper mulberry trees in order to reconstruct Jefferson's plantation.

[Sectional structure of a tree. Model analysis of the vertical biomass distribution].

PubMed

Galitskiĭ, V V

2010-01-01

A model has been proposed for the architecture of a tree in which virtual trees appear rhythmically on the treetop. Each consecutive virtual tree is a part of the previous tree. The difference between two adjacent virtual trees is a section--an element of the real tree structure. In case of a spruce, the section represents a verticil of a stem with the corresponding internode. Dynamics of a photosynthesizing part of the physiologically active biomass of each section differ from the corresponding dynamics of the virtual trees and the whole real tree. If the tree biomass dynamics has a sigma-shaped form, then the section dynamics have to be bell-shaped. It means that the lower stem should accordingly become bare, which is typically observed in nature. Model analysis reveals the limiting, in the age, form of trees to be an "umbrella". It can be observed in nature and is an outcome of physical limitation of the tree height combined with the sigma-shaped form of the tree biomass dynamics. Variation of model parameters provides for various forms of the tree biomass distribution along the height, which can be associated with certain biological species of trees.

Identification and Mapping of Tree Species in Urban Areas Using WORLDVIEW-2 Imagery

NASA Astrophysics Data System (ADS)

Mustafa, Y. T.; Habeeb, H. N.; Stein, A.; Sulaiman, F. Y.

2015-10-01

Monitoring and mapping of urban trees are essential to provide urban forestry authorities with timely and consistent information. Modern techniques increasingly facilitate these tasks, but require the development of semi-automatic tree detection and classification methods. In this article, we propose an approach to delineate and map the crown of 15 tree species in the city of Duhok, Kurdistan Region of Iraq using WorldView-2 (WV-2) imagery. A tree crown object is identified first and is subsequently delineated as an image object (IO) using vegetation indices and texture measurements. Next, three classification methods: Maximum Likelihood, Neural Network, and Support Vector Machine were used to classify IOs using selected IO features. The best results are obtained with Support Vector Machine classification that gives the best map of urban tree species in Duhok. The overall accuracy was between 60.93% to 88.92% and κ-coefficient was between 0.57 to 0.75. We conclude that fifteen tree species were identified and mapped at a satisfactory accuracy in urban areas of this study.

Vulnerabilities, Influences and Interaction Paths: Failure Data for Integrated System Risk Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Fleming, Land

2006-01-01

We describe graph-based analysis methods for identifying and analyzing cross-subsystem interaction risks from subsystem connectivity information. By discovering external and remote influences that would be otherwise unexpected, these methods can support better communication among subsystem designers at points of potential conflict and to support design of more dependable and diagnosable systems. These methods identify hazard causes that can impact vulnerable functions or entities if propagated across interaction paths from the hazard source to the vulnerable target. The analysis can also assess combined impacts of And-Or trees of disabling influences. The analysis can use ratings of hazards and vulnerabilities to calculate cumulative measures of the severity and importance. Identification of cross-subsystem hazard-vulnerability pairs and propagation paths across subsystems will increase coverage of hazard and risk analysis and can indicate risk control and protection strategies.

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.

PubMed

Speiser, Daniel I; Pankey, M Sabrina; Zaharoff, Alexander K; Battelle, Barbara A; Bracken-Grissom, Heather D; Breinholt, Jesse W; Bybee, Seth M; Cronin, Thomas W; Garm, Anders; Lindgren, Annie R; Patel, Nipam H; Porter, Megan L; Protas, Meredith E; Rivera, Ajna S; Serb, Jeanne M; Zigler, Kirk S; Crandall, Keith A; Oakley, Todd H

2014-11-19

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository ( http://bitbucket.org/osiris_phylogenetics/pia/ ) and we demonstrate PIA on a publicly-accessible web server ( http://galaxy-dev.cnsi.ucsb.edu/pia/ ). Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.

Insight into the hydraulics and resilience of Ponderosa pine seedlings using a mechanistic ecohydrologic model

NASA Astrophysics Data System (ADS)

Maneta, M. P.; Simeone, C.; Dobrowski, S.; Holden, Z.; Sapes, G.; Sala, A.; Begueria, S.

2017-12-01

In semiarid regions, drought-induced seedling mortality is considered to be caused by failure in the tree hydraulic column. Understanding the mechanisms that cause hydraulic failure and death in seedlings is important, among other things, to diagnose where some tree species may fail to regenerate, triggering demographic imbalances in the forest that could result in climate-driven shifts of tree species. Ponderosa pine is a common lower tree line species in the western US. Seedlings of ponderosa pine are often subject to low soil water potentials, which require lower water potentials in the xylem and leaves to maintain the negative pressure gradient that drives water upward. The resilience of the hydraulic column to hydraulic tension is species dependent, but from greenhouse experiments, we have identified general tension thresholds beyond which loss of xylem conductivity becomes critical, and mortality in Ponderosa pine seedlings start to occur. We describe this hydraulic behavior of plants using a mechanistic soil-vegetation-atmosphere transfer model. Before we use this models to understand water-stress induced seedling mortality at the landscape scale, we perform a modeling analysis of the dynamics of soil moisture, transpiration, leaf water potential and loss of plant water conductivity using detailed data from our green house experiments. The analysis is done using a spatially distributed model that simulates water fluxes, energy exchanges and water potentials in the soil-vegetation-atmosphere continuum. Plant hydraulic and physiological parameters of this model were calibrated using Monte Carlo methods against information on soil moisture, soil hydraulic potential, transpiration, leaf water potential and percent loss of conductivity in the xylem. This analysis permits us to construct a full portrait of the parameter space for Ponderosa pine seedling and generate posterior predictive distributions of tree response to understand the sensitivity of transpiration, hydraulic tension in the plant, and percent loss of conductivity to environmental stresses.

Vector Analysis Identify Loblolly Pine (Pinus taeda L.) Phosphorus Deficiency on a Beauregard Soil

Treesearch

A. Bekele; W.H. Hundall; A.E. Tiarks

1999-01-01

We studied the response of densely stocked one-year-old loblolly pine (Pinus taeda L.) to N and P fertilizers on a Beauregard silt loam (fine silty, siliceous, thermic, Plinthaquic Paleudults). A continuous function" experimental design with three replications was used. Each replication consisted of 12 m X 12 m plots, with three trees planted...

RNA-seq analysis of developing pecan (Carya illinoinensis) embryos reveals parallel expression patterns among allergen and lipid metabolism genes

USDA-ARS?s Scientific Manuscript database

Pecan nuts and other tree nuts can be a nutrient rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. We characterized the transcriptome of a developing pecan nut to identify the gene ex...

Ten-year results of a ponderosa pine progeny test in the Black Hills

Treesearch

Wayne D. Shepperd; Sue E. McElderry

1986-01-01

Ten-year survival and growth of seedlings from 77 parent trees from throughout the Black Hills were compared, using a cluster-analysis technique. Five clusters were identified that account for most of the variability in survival and growth of the open-pollinated families. One cluster, containing 6 families, exhibited exceptional survival and growth. Another, containing...

An Evaluation of Risk Factors Related to Employment Outcomes for Youth with Disabilities

ERIC Educational Resources Information Center

Sima, Adam P.; Wehman, Paul H.; Chan, Fong; West, Michael D.; Leucking, Richard G.

2015-01-01

This study explores non-modifiable risk factors associated with poor post-school competitive employment outcomes for students with disabilities. A classification tree analysis was used with a sample of 2,900 students who were in the second National Longitudinal Transition Study-2 (NLTS2) up to 6 years following school exit to identify groups of…

Identifying changes in tree form for harvested ponderosa pine in the Black Hills

Treesearch

Michael S. Williams; Raymond L. Czaplewski; Don L. Martinez

1996-01-01

Recent underestimates of total volume for timber sales in the Black Hills National Forest prompted analysis of two felled ponderosa pine (Pinus ponderosa Laws.) data sets that were collected approximately 10 years apart. Though neither data set collected was a representative sample of the Black Hills, both were similar in terms of diameter at breast height and total...

User guide for HCR Estimator 2.0: software to calculate cost and revenue thresholds for harvesting small-diameter ponderosa pine.

Treesearch

Dennis R. Becker; Debra Larson; Eini C. Lowell; Robert B. Rummer

2008-01-01

The HCR (Harvest Cost-Revenue) Estimator is engineering and financial analysis software used to evaluate stand-level financial thresholds for harvesting small-diameter ponderosa pine (Pinus ponderosa Dougl. ex Laws.) in the Southwest United States. The Windows-based program helps contractors and planners to identify costs associated with tree...

Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis

PubMed Central

Hsu, Kuo-Hsiang; Su, Bo-Han; Tu, Yi-Shu; Lin, Olivia A.; Tseng, Yufeng J.

2016-01-01

With advances in the development and application of Ames mutagenicity in silico prediction tools, the International Conference on Harmonisation (ICH) has amended its M7 guideline to reflect the use of such prediction models for the detection of mutagenic activity in early drug safety evaluation processes. Since current Ames mutagenicity prediction tools only focus on functional group alerts or side chain modifications of an analog series, these tools are unable to identify mutagenicity derived from core structures or specific scaffolds of a compound. In this study, a large collection of 6512 compounds are used to perform scaffold tree analysis. By relating different scaffolds on constructed scaffold trees with Ames mutagenicity, four major and one minor novel mutagenic groups of scaffold are identified. The recognized mutagenic groups of scaffold can serve as a guide for medicinal chemists to prevent the development of potentially mutagenic therapeutic agents in early drug design or development phases, by modifying the core structures of mutagenic compounds to form non-mutagenic compounds. In addition, five series of substructures are provided as recommendations, for direct modification of potentially mutagenic scaffolds to decrease associated mutagenic activities. PMID:26863515

Using Decision Tree Analysis to Understand Foundation Science Student Performance. Insight Gained at One South African University

NASA Astrophysics Data System (ADS)

Kirby, Nicola Frances; Dempster, Edith Roslyn

2014-11-01

The Foundation Programme of the Centre for Science Access at the University of KwaZulu-Natal, South Africa provides access to tertiary science studies to educationally disadvantaged students who do not meet formal faculty entrance requirements. The low number of students proceeding from the programme into mainstream is of concern, particularly given the national imperative to increase participation and levels of performance in tertiary-level science. An attempt was made to understand foundation student performance in a campus of this university, with the view to identifying challenges and opportunities for remediation in the curriculum and processes of selection into the programme. A classification and regression tree analysis was used to identify which variables best described student performance. The explanatory variables included biographical and school-history data, performance in selection tests, and socio-economic data pertaining to their year in the programme. The results illustrate the prognostic reliability of the model used to select students, raise concerns about the inefficiency of school performance indicators as a measure of students' academic potential in the Foundation Programme, and highlight the importance of accommodation arrangements and financial support for student success in their access year.

Narrowing historical uncertainty: probabilistic classification of ambiguously identified tree species in historical forest survey data

USGS Publications Warehouse

Mladenoff, D.J.; Dahir, S.E.; Nordheim, E.V.; Schulte, L.A.; Guntenspergen, G.R.

2002-01-01

Historical data have increasingly become appreciated for insight into the past conditions of ecosystems. Uses of such data include assessing the extent of ecosystem change; deriving ecological baselines for management, restoration, and modeling; and assessing the importance of past conditions on the composition and function of current systems. One historical data set of this type is the Public Land Survey (PLS) of the United States General Land Office, which contains data on multiple tree species, sizes, and distances recorded at each survey point, located at half-mile (0.8 km) intervals on a 1-mi (1.6 km) grid. This survey method was begun in the 1790s on US federal lands extending westward from Ohio. Thus, the data have the potential of providing a view of much of the US landscape from the mid-1800s, and they have been used extensively for this purpose. However, historical data sources, such as those describing the species composition of forests, can often be limited in the detail recorded and the reliability of the data, since the information was often not originally recorded for ecological purposes. Forest trees are sometimes recorded ambiguously, using generic or obscure common names. For the PLS data of northern Wisconsin, USA, we developed a method to classify ambiguously identified tree species using logistic regression analysis, using data on trees that were clearly identified to species and a set of independent predictor variables to build the models. The models were first created on partial data sets for each species and then tested for fit against the remaining data. Validations were conducted using repeated, random subsets of the data. Model prediction accuracy ranged from 81% to 96% in differentiating congeneric species among oak, pine, ash, maple, birch, and elm. Major predictor variables were tree size, associated species, landscape classes indicative of soil type, and spatial location within the study region. Results help to clarify ambiguities formerly present in maps of historic ecosystems for the region and can be applied to PLS datasets elsewhere, as well as other sources of ambiguous historical data. Mapping the newly classified data with ecological land units provides additional information on the distribution, abundance, and associations of tree species, as well as their relationships to environmental gradients before the industrial period, and clarifies the identities of species formerly mapped only to genus. We offer some caveats on the appropriate use of data derived in this way, as well as describing their potential.

Transcriptomic Analysis of Paeonia delavayi Wild Population Flowers to Identify Differentially Expressed Genes Involved in Purple-Red and Yellow Petal Pigmentation

PubMed Central

Wang, Yan; Li, Kui; Zheng, Baoqiang; Miao, Kun

2015-01-01

Tree peony (Paeonia suffruticosa Andrews) is a very famous traditional ornamental plant in China. P. delavayi is a species endemic to Southwest China that has aroused great interest from researchers as a precious genetic resource for flower color breeding. However, the current understanding of the molecular mechanisms of flower pigmentation in this plant is limited, hindering the genetic engineering of novel flower color in tree peonies. In this study, we conducted a large-scale transcriptome analysis based on Illumina HiSeq sequencing of cDNA libraries generated from yellow and purple-red P. delavayi petals. A total of 90,202 unigenes were obtained by de novo assembly, with an average length of 721 nt. Using Blastx, 44,811 unigenes (49.68%) were found to have significant similarity to accessions in the NR, NT, and Swiss-Prot databases. We also examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Further analysis of the two digital transcriptomes revealed that 6,855 unigenes were differentially expressed between yellow and purple-red flower petals, with 3,430 up-regulated and 3,425 down-regulated. According to the RNA-Seq data and qRT-PCR analysis, we proposed that four up-regulated key structural genes, including F3H, DFR, ANS and 3GT, might play an important role in purple-red petal pigmentation, while high co-expression of THC2'GT, CHI and FNS II ensures the accumulation of pigments contributing to the yellow color. We also found 50 differentially expressed transcription factors that might be involved in flavonoid biosynthesis. This study is the first to report genetic information for P. delavayi. The large number of gene sequences produced by transcriptome sequencing and the candidate genes identified using pathway mapping and expression profiles will provide a valuable resource for future association studies aimed at better understanding the molecular mechanisms underlying flower pigmentation in tree peonies. PMID:26267644

Identifying stressed and potentially unstable trees by aerial photography on Ohio's highways.

DOT National Transportation Integrated Search

2002-10-01

Trees are valuable assets and potential liabilities in a man dominated situations such as : along Ohios highways. While trees are often long-lived, they must decline and die like : any other living thing. Decline may be nearly instantaneous as in ...

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas.

PubMed

Vinuesa, Pablo; Ochoa-Sánchez, Luz E; Contreras-Moreira, Bruno

2018-01-01

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia , demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

PubMed Central

Shade, Ashley; McManus, Patricia S.; Handelsman, Jo

2013-01-01

ABSTRACT Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. PMID:23443006

Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea.

PubMed

Miller, Allison; Schaal, Barbara

2005-09-06

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (Spondias purpurea), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer trnG-trnS were obtained for cultivated and wild S. purpurea trees, two sympatric taxa (Spondias mombin var. mombin and Spondias radlkoferi), and two outgroups (S. mombin var. globosa and Spondias testudinus). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of S. purpurea are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in S. purpurea trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated S. purpurea populations have fewer unique trnG-trnS alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in S. purpurea.

Using EnviroAtlas to Identify Locations for Urban Heat Island Abatement

EPA Science Inventory

For the metropolitan region of Portland, Oregon, this use case demonstrates how city planners could use EnviroAtlas data with a map of the UHI to identify areas that might benefit from heat mitigation through additional street trees. Street trees are one option, and other solutio...

Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea

PubMed Central

Miller, Allison; Schaal, Barbara

2005-01-01

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (Spondias purpurea), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer trnG–trnS were obtained for cultivated and wild S. purpurea trees, two sympatric taxa (Spondias mombin var. mombin and Spondias radlkoferi), and two outgroups (S. mombin var. globosa and Spondias testudinus). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of S. purpurea are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in S. purpurea trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated S. purpurea populations have fewer unique trnG–trnS alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in S. purpurea. PMID:16126899

Unique haplotypes of cacao trees as revealed by trnH-psbA chloroplast DNA

PubMed Central

Gutiérrez-López, Nidia; Ovando-Medina, Isidro; Salvador-Figueroa, Miguel; Molina-Freaner, Francisco; Avendaño-Arrazate, Carlos H.

2016-01-01

Cacao trees have been cultivated in Mesoamerica for at least 4,000 years. In this study, we analyzed sequence variation in the chloroplast DNA trnH-psbA intergenic spacer from 28 cacao trees from different farms in the Soconusco region in southern Mexico. Genetic relationships were established by two analysis approaches based on geographic origin (five populations) and genetic origin (based on a previous study). We identified six polymorphic sites, including five insertion/deletion (indels) types and one transversion. The overall nucleotide diversity was low for both approaches (geographic = 0.0032 and genetic = 0.0038). Conversely, we obtained moderate to high haplotype diversity (0.66 and 0.80) with 10 and 12 haplotypes, respectively. The common haplotype (H1) for both networks included cacao trees from all geographic locations (geographic approach) and four genetic groups (genetic approach). This common haplotype (ancient) derived a set of intermediate haplotypes and singletons interconnected by one or two mutational steps, which suggested directional selection and event purification from the expansion of narrow populations. Cacao trees from Soconusco region were grouped into one cluster without any evidence of subclustering based on AMOVA (FST = 0) and SAMOVA (FST = 0.04393) results. One population (Mazatán) showed a high haplotype frequency; thus, this population could be considered an important reservoir of genetic material. The indels located in the trnH-psbA intergenic spacer of cacao trees could be useful as markers for the development of DNA barcoding. PMID:27076998

Underground riparian wood: Reconstructing the processes influencing buried stem and coarse root structures of Black Poplar (Populus nigra L.)

NASA Astrophysics Data System (ADS)

Holloway, James V.; Rillig, Matthias C.; Gurnell, Angela M.

2017-02-01

Following analysis of morphological (including dendrochronological and sedimentological) aspects of buried stem and coarse root structures of eight mature P. nigra individuals located within two sites along the middle to lower Tagliamento River, Italy (Holloway et al., 2017), this paper introduces information on the historical processes of vegetation development and river flow and links this to the form of these eight trees. Aerial images and flow time series are assembled to reconstruct the flood history, potential recruitment periods, and vegetation cover development in the vicinity of the studied trees. This information is combined with previous morphological evidence to reconstruct the development history of each tree via three-element summary diagrams showing (i) a time series of floods, aerial imagery dates, and potential recruitment periods, with colour-coded bars indicating likely key stages in the development of the tree; (ii) colour-coded overlays on an SfM photogrammetric model of each tree; and (iii) colour-coded text boxes providing explanatory annotations. The combined morphology-process analysis reveals complex three-dimensional underground structures, incorporating buried stems, shoots, and adventitious roots that are sometimes joined by grafting, linking the standing tree with the buried gravel surface on which it was recruited. Analysis of process data provides a firm basis for identifying and dating influential flow disturbance events and recruitment windows and shows that a relatively small number of flood events have significantly impacted the studied trees, which are mainly but not exclusively the largest floods in the record. Nevertheless, we stress that all suggested dates are best estimates in the light of the combined evidence. There is undoubted potential for building different interpretations of belowground woody structure development in light of such evidence, but we feel that the form and timing of the developmental trajectories we have proposed are reasonable and give balanced insights into the many possible ways in which this hidden component of riparian trees may develop. Our results are relevant to river research and management issues concerning riparian woodland, fluvial wood dynamics, and wood budgets, as they indicate (i) a large hidden volume of wood that is often ignored; (ii) complex, deep, coarse anchorage structures that have relevance for rates of fluvial wood recruitment associated with lateral bank erosion/stability or wind throw; and (iii) a wood element that may significantly affect wood transport and retention within fluvial systems.

Fault Tree Analysis: Its Implications for Use in Education.

ERIC Educational Resources Information Center

Barker, Bruce O.

This study introduces the concept of Fault Tree Analysis as a systems tool and examines the implications of Fault Tree Analysis (FTA) as a technique for isolating failure modes in educational systems. A definition of FTA and discussion of its history, as it relates to education, are provided. The step by step process for implementation and use of…

Species Composition of Down Dead and Standing Live Trees: Implications for Forest Inventory Analysis

Treesearch

Christopher W. Woodall; Linda Nagel

2005-01-01

The assessment of species composition in most forest inventory analysis relies solely on standing live tree information characterized by current forest type. With the implementation of the third phase of the U.S. Department of Agriculture Forest Service's Forest Inventory and Analysis program, the species composition of down dead trees, otherwise termed coarse...

Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth.

PubMed

Liu, Jinwen; Hai, Guanghui; Wang, Chong; Cao, Shenquan; Xu, Wenjing; Jia, Zhigang; Yang, Chuanping; Wang, Jack P; Dai, Shaojun; Cheng, Yuxiang

2015-08-03

Wood is derived from the secondary growth of tree stems. In this study, we investigated the global changes of protein abundance in Populus early stems using a proteomic approach. Morphological and histochemical analyses revealed three typical stages during Populus early stems, which were the primary growth stage, the transition stage from primary to secondary growth and the secondary growth stage. A total of 231 spots were differentially abundant during various growth stages of Populus early stems. During Populus early stem lignifications, 87 differential spots continuously increased, while 49 spots continuously decreased. These two categories encompass 58.9% of all differential spots, which suggests significant molecular changes from primary to secondary growth. Among 231 spots, 165 unique proteins were identified using LC-ESI-Q-TOF-MS, which were classified into 14 biological function groups. The proteomic characteristics indicated that carbohydrate metabolism, oxido-reduction, protein degradation and secondary cell wall metabolism were the dominantly occurring biochemical processes during Populus early stem development. This study helps in elucidating biochemical processes and identifies potential wood formation-related proteins during tree early stem development. It is a comprehensive proteomic investigation on tree early stem development that, for the first time, reveals the overall molecular networks that occur during Populus early stem lignifications. Copyright © 2015. Published by Elsevier B.V.

Comparative Analysis of Latex Transcriptome Reveals Putative Molecular Mechanisms Underlying Super Productivity of Hevea brasiliensis

PubMed Central

Li, Heping; Fan, Yujie; Yang, Jianghua; Qi, Jiyan; Li, Huibo

2013-01-01

Increasing demand for natural rubber prompts studies into the mechanisms governing the productivity of rubber tree ( Hevea brasiliensis ). It is very interesting to notice that a rubber tree of clone PR107 in Yunnan, China is reported to yield more than 20 times higher than the average rubber tree. This super-high-yielding (SHY) rubber tree (designated as SY107), produced 4.12 kg of latex (cytoplasm of rubber producing laticifers, containing about 30% of rubber) per tapping, more than 7-fold higher than that of the control. This rubber tree is therefore a good material to study how the rubber production is regulated at a molecular aspect. A comprehensive cDNA-AFLP transcript profiling was performed on the latex of SY107 and its average counterparts by using the 384 selective primer pairs for two restriction enzyme combinations (ApoI/MseI and TaqI/MseI). A total of 746 differentially expressed (DE) transcript-derived fragments (TDFs) were identified, of which the expression patterns of 453 TDFs were further confirmed by RT-PCR. These RT-PCR confirmed TDFs represented 352 non-redundant genes, of which 215 had known or partially known functions and were grouped into 10 functional categories. The top three largest categories were transcription and protein synthesis (representing 24.7% of the total genes), defense and stress (15.3%), and primary and secondary metabolism (14.0%). Detailed analysis of the DE-genes suggests notable characteristics of SHY phenotype in improved sucrose loading capability, rubber biosynthesis-preferred sugar utilization, enhanced general metabolism and timely stress alleviation. However, the SHY phenotype has little correlation with rubber-biosynthesis pathway genes. PMID:24066172

A Changing Number of Alternative States in the Boreal Biome: Reproducibility Risks of Replacing Remote Sensing Products.

PubMed

Xu, Chi; Holmgren, Milena; Van Nes, Egbert H; Hirota, Marina; Chapin, F Stuart; Scheffer, Marten

2015-01-01

Publicly available remote sensing products have boosted science in many ways. The openness of these data sources suggests high reproducibility. However, as we show here, results may be specific to versions of the data products that can become unavailable as new versions are posted. We focus on remotely-sensed tree cover. Recent studies have used this public resource to detect multi-modality in tree cover in the tropical and boreal biomes. Such patterns suggest alternative stable states separated by critical tipping points. This has important implications for the potential response of these ecosystems to global climate change. For the boreal region, four distinct ecosystem states (i.e., treeless, sparse and dense woodland, and boreal forest) were previously identified by using the Collection 3 data of MODIS Vegetation Continuous Fields (VCF). Since then, the MODIS VCF product has been updated to Collection 5; and a Landsat VCF product of global tree cover at a fine spatial resolution of 30 meters has been developed. Here we compare these different remote-sensing products of tree cover to show that identification of alternative stable states in the boreal biome partly depends on the data source used. The updated MODIS data and the newer Landsat data consistently demonstrate three distinct modes around similar tree-cover values. Our analysis suggests that the boreal region has three modes: one sparsely vegetated state (treeless), one distinct 'savanna-like' state and one forest state, which could be alternative stable states. Our analysis illustrates that qualitative outcomes of studies may change fundamentally as new versions of remote sensing products are used. Scientific reproducibility thus requires that old versions remain publicly available.

Automated identification of best-quality coronary artery segments from multiple-phase coronary CT angiography (cCTA) for vessel analysis

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Chughtai, Aamer; Wei, Jun; Kazerooni, Ella A.

2016-03-01

We are developing an automated method to identify the best quality segment among the corresponding segments in multiple-phase cCTA. The coronary artery trees are automatically extracted from different cCTA phases using our multi-scale vessel segmentation and tracking method. An automated registration method is then used to align the multiple-phase artery trees. The corresponding coronary artery segments are identified in the registered vessel trees and are straightened by curved planar reformation (CPR). Four features are extracted from each segment in each phase as quality indicators in the original CT volume and the straightened CPR volume. Each quality indicator is used as a voting classifier to vote the corresponding segments. A newly designed weighted voting ensemble (WVE) classifier is finally used to determine the best-quality coronary segment. An observer preference study is conducted with three readers to visually rate the quality of the vessels in 1 to 6 rankings. Six and 10 cCTA cases are used as training and test set in this preliminary study. For the 10 test cases, the agreement between automatically identified best-quality (AI-BQ) segments and radiologist's top 2 rankings is 79.7%, and between AI-BQ and the other two readers are 74.8% and 83.7%, respectively. The results demonstrated that the performance of our automated method was comparable to those of experienced readers for identification of the best-quality coronary segments.

Adjustments to forest inventory and analysis estimates of 2001 saw-log volumes for Kentucky

Treesearch

Stanley J. Zarnoch; Jeffery A. Turner

2005-01-01

The 2001 Kentucky Forest Inventory and Analysis survey overestimated hardwood saw-log volume in tree grade 1. This occurred because 2001 field crews classified too many trees as grade 1 trees. Data collected by quality assurance crews were used to generate two types of adjustments, one based on the proportion of trees misclassified and the other on the proportion of...

ETE: a python Environment for Tree Exploration.

PubMed

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

Environmental justice and factors that influence participation in tree planting programs in Portland, Oregon, U.S

Treesearch

Geoffrey H. Donovan; John Mills

2014-01-01

Many cities have policies encouraging homeowners to plant trees. For these policies to be effective, it is important to understand what motivates a homeowner’s tree-planting decision. Researchers address this question by identifying variables that influence participation in a tree-planting program in Portland, Oregon, U.S. According to the study, homeowners with street...

Structure, function and value of street trees in California, USA

Treesearch

E. Gregory McPherson; Natalie van Doorn; John de Goede

2016-01-01

This study compiled recent inventory data from 929,823 street trees in 50 cities to determine trends in tree number and density, identify priority investments and create baseline data against which the efficacy of future practices can be evaluated. The number of street trees increased from 5.9 million in 1988 to 9.1 million in 2014, about one for every four residents....

A method for locating potential tree-planting sites in urban areas: a case study of Los Angeles, USA

Treesearch

Chunxia Wua; Qingfu Xiaoa; Gregory E. McPherson

2008-01-01

A GIS-based method for locating potential tree-planting sites based on land cover data is introduced. Criteria were developed to identify locations that are spatially available for potential tree planting based on land cover, sufficient distance from impervious surfaces, a minimum amount of pervious surface, and no crown overlap with other trees. In an ArcGIS...